Dictionary of Mass Spectrometry
Dictionary of Mass Spectrometry A.I. Mallet and S. Down
A John Wiley and Sons, Ltd., Publication
This edition first published 2009 © 2009 John Wiley & Sons Ltd Registered office John Wiley & Sons Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, United Kingdom For details of our global editorial offices, for customer services and for information about how to apply for permission to reuse the copyright material in this book please see our website at www.wiley.com. The right of the author to be identified as the author of this work has been asserted in accordance with the Copyright, Designs and Patents Act 1988. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher. Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books. Designations used by companies to distinguish their products are often claimed as trademarks. All brand names and product names used in this book are trade names, service marks, trademarks or registered trademarks of their respective owners. The publisher is not associated with any product or vendor mentioned in this book. This publication is designed to provide accurate and authoritative information in regard to the subject matter covered. It is sold on the understanding that the publisher is not engaged in rendering professional services. If professional advice or other expert assistance is required, the services of a competent professional should be sought. The publisher and the author make no representations or warranties with respect to the accuracy or completeness of the contents of this work and specifically disclaim all warranties, including without limitation any implied warranties of fitness for a particular purpose. This work is sold with the understanding that the publisher is not engaged in rendering professional services. The advice and strategies contained herein may not be suitable for every situation. In view of ongoing research, equipment modifications, changes in governmental regulations, and the constant flow of information relating to the use of experimental reagents, equipment, and devices, the reader is urged to review and evaluate the information provided in the package insert or instructions for each chemical, piece of equipment, reagent, or device for, among other things, any changes in the instructions or indication of usage and for added warnings and precautions. The fact that an organization or Website is referred to in this work as a citation and/or a potential source of further information does not mean that the author or the publisher endorses the information the organization or Website may provide or recommendations it may make. Further, readers should be aware that Internet Websites listed in this work may have changed or disappeared between when this work was written and when it is read. No warranty may be created or extended by any promotional statements for this work. Neither the publisher nor the author shall be liable for any damages arising herefrom. Library of Congress Cataloging-in-Publication Data Mallet, Anthony. Dictionary of mass spectrometry / Anthony Mallet and Stephen Down. p. cm. Includes bibliographical references. ISBN 978-0-470-02761-5 (pbk. : alk. paper) 1. Mass spectrometry--Dictionaries. I. Down, Stephen. II. Title. QD96.M3M3336 2009 543'.6503--dc22 2009017126 A catalogue record for this book is available from the British Library. ISBN 978-0-470-02761-5 Set in 11pt Frutiger 65 Bold and 10pt Times New Roman by Micropress Printed in the UK by Micropress, 27 Norwich Road, Halesworth, Suffolk, IP19 8BX
Contents Preface
vi
Sponsors
vii
Acronyms
1
Dictionary Entries
5
Suggested Reading
170
Sponsor Information
172
Preface The Dictionary of Mass Spectrometry is intended to act as a first point of reference for explanations of the common terms and acronyms used in current practice of mass spectrometry. It is aimed at newcomers to mass spectrometry as well as experienced practitioners, covering new and established terminology that is encountered in the literature. The book follows the format of the Dictionary of Microscopy, the entries being accompanied by many illustrations, diagrams and photographs for clarification. The entries are explanations, not definitions, and a deliberately non-judgemental approach has been followed. For an account of the preferred or accepted terms, there are a number of texts, some listed in the suggested reading list, which fulfil this purpose. This content of this book is not exhaustive. New terms and techniques will appear in the future and the authors welcome suggestions for additions, as well as any corrections and comments on the existing entries. The authors are indebted to their colleagues and especially to Dr Bob Boyd and Dr Gareth Brenton for their helpful comments. Tony Mallet Steve Down July 2009
vi
Sponsors Gold Sponsors: Thermo Electron (USA)
Sponsors: In House Gas Ltd Jeol USA Inc SGE Europe Ltd Thermo Fisher (UK) Waters Corporation
vii
Acronyms This list contains many of the acronyms encountered in mass spectrometry. They are also defined at the appropriate entry in the listings. AC ADC AMDIS AMS AP APCI API APPI BIA BIRD CAD CE CI CID CNL CRIMS CRM DAC DAD DART DBDI DBE DC DCI DEI DEP DESI DIOS DLI DMS DNA ECD
alternating current analogue-to-digital converter automated mass spectral deconvolution and identification system accelerator mass spectrometry atmospheric pressure atmospheric pressure chemical ionisation atmospheric pressure ionisation atmospheric pressure photoionisation biomolecular interaction analysis blackbody infrared radiative dissociation collisionally activated dissociation capillary electrophoresis chemical ionisation collision-induced dissociation constant neutral loss chemical reaction interface mass spectrometry certified reference material digital-to-analogue converter diode array detector direct analysis in real time dielectric barrier discharge ionisation double bond equivalent direct current desorption chemical ionisation desorption electron ionisation direct exposure probe desorption electrospray ionisation desorption/ionisation on silicon direct liquid introduction differential mobility spectrometry deoxyribonucleic acid electron capture dissociation 1
acronyms
EI electron ionisation EM electron multiplier ESA electrostatic energy analyser ESI electrospray ionisation ESSI electrosonic spray ionisation ETD electron transfer dissociation FAB fast atom bombardment FAIMS high-field asymmetric waveform ion mobility spectrometry FD field desorption FFR field-free region FI field ionisation FIA flow injection analysis FID free induction decay FNF filtered noise field FT Fourier transform FTICR Fourier transform/ion cyclotron resonance FWHM full width at half-maximum height GC gas chromatography GC-C-IRMS or GCC-IRMS gas chromatography-combustion-isotope ratio mass spectrometry GC/MS gas chromatography/mass spectrometry GDMS glow discharge mass spectrometry GPC gel permeation chromatography HDX hydrogen/deuterium exchange HPLC high performance liquid chromatography ICAT isotope-coded affinity tag ICP inductively coupled plasma ICPMS inductively coupled plasma mass spectrometry ICR ion cyclotron resonance IDA information-dependent acquisition IKES ion kinetic energy spectrometry IMS ion mobility spectrometry IR infrared IRMPD infrared multiphoton dissociation IRMS isotope ratio mass spectrometry JeDI jet desorption ionisation LAMMA laser-activated microprobe mass analysis 2
acronyms
LC LC/MS LC/MS/MS LDI LIT LLOD LLOQ LOD LOQ LSIMS MALDI MECA MIKES MIMS MRM MS MS/MS MudPIT NALDI NICI NIST PA PAD PBM PCA PCR PDA PICI PID PSD PTM PTR QIT QTOF QUISTOR RDBE REMPI
liquid chromatography liquid chromatography/mass spectrometry liquid chromatography/mass spectrometry/mass spectrometry laser desorption/ionisation linear ion trap lower limit of detection lower limit of quantitation limit of detection limit of quantitation liquid secondary ionisation mass spectrometry matrix-assisted laser desorption/ionisation multiple excitation collisional activation mass-analysed ion kinetic energy spectrometry membrane introduction mass spectrometry multiple reaction monitoring mass spectrometry mass spectrometry/mass spectrometry multidimensional protein identification technology nano-assisted laser desorption/ionisation negative ion chemical ionisation National Institute of Standards and Technology proton affinity post-acceleration detector probability based matching principal components analysis polymerase chain reaction photodiode array detector positive ion chemical ionisation photon-induced dissociation post-source decay post-translational modification proton transfer reaction quadrupole ion trap quadrupole time-of-flight quadrupole ion storage trap rings and double bond equivalents resonance-enhanced multiphoton ionisation 3
acronyms
RF RGA RIC RMM RNA RRKM SALDI SDS-PAGE SELDI SIC SID SIFT SILAC SIM SIMION SIMS SIR SIRA SNMS SORI SPR SQUID SRM SSI SWIFT TDC TES TIC TICC TLC TOF TSP UV XIC
4
radiofrequency residual gas analyser reconstructed ion chromatogram relative molecular mass ribonucleic acid Rice, Ramsperger, Kassel, Marcus surface-assisted laser desorption/ionisation sodium dodecyl sulfate polyacrylamide gel electrophoresis surface-enhanced laser desorption/ionisation selected ion chromatogram surface-induced dissociation selected ion flow tube stable isotope labelling of amino acids in cell culture selected ion monitoring simulated ion trajectory algorithm secondary ion mass spectrometry selected ion recording stable isotope ratio analysis secondary neutral mass spectrometry sustained off-resonance irradiation surface plasmon resonance superconducting tunnel junction detector selected reaction monitoring sonic spray ionisation stored waveform inverse Fourier transform time-to-digital converter translational energy loss spectrometry total ion current or total ion chromatogram total ion current chromatogram thin-layer chromatography time of flight thermospray ionisation ultraviolet extracted ion chromatogram
an ion
A an ion An N-terminal ion formed by fission of a peptide ion at the C-C peptide bond. See peptide sequencing
au Parameter in the Mathieu equation. See Mathieu stability diagram
abundance This term is used to describe the relative occurrence of an ion. A mass spectrum is a plot of the ion abundances against the m/z values determined and is normalised to the most abundant ion. This term should be distinguished from intensity which, while appropriate for the signal of the individual ion peak detected, is not used in spectra.
accelerating voltage (V) The potential applied to newly formed ions in the mass spectrometer source to direct them into the analyser. 5
accelerating voltage scan accelerating voltage scan A scan mode for relatively rapid scanning of a magnetic sector instrument where, over a limited m/z range, the accelerating voltage is scanned while the magnetic field is held constant. This obviates the problems associated with hysteresis and inherent resistance to rapid changes in the magnetic field but also defocusses the ion source. See also defocussing voltage scan
accelerator MS (AMS)
Accelerator MS, National Electrostatics Corporation
A technique for the determination of precise isotope ratios for elements of very low abundance, principally 14C isotopes but increasingly also 3H, 41Ca and 26Al. The element to be analysed is extracted from the sample and inserted in the ion source in a metal holder. It is bombarded with a beam of caesium ions (Cs+) to produce negative ions which are passed through a magnetic field for ion selection. The resultant ions are accelerated to high energy, typically >1 MeV, in a tandem accelerator in which charge stripping occurs to convert the negative ions to positive ions. This will minimise cross talk from other isobaric ions. A sequence of analyser elements is employed to produce signals of high specificity. The method is used in archaeology, geophysics and clinical chemistry.
accuracy The accuracy of a mass measurement or concentration from a quantitative determination is a measure of how close the value obtained is to the true value. See also precision
accurate mass measurement An experimental determination of the accurate and precise value of m/z for an ion, usually with a view to suggesting elemental composition.
accurate molecular mass The measured mass of a molecule or ion determined with sufficent accuracy to allow the determination of a probable elemental composition.
6
acidic residue acidic residue An amino acid residue in a peptide or protein that has an acidic nature, such as aspartic acid or glutamic acid.
adduct ion An electrically charged species formed by noncovalent attachment between an ion and a neutral species. These are most commonly observed in desorption and API and CI ion sources where a molecule of a component in the solvent or reagent gas remains attached to the ion. The illustration shows the formation of a formic acid adduct ion from the negative ESI of a carboxylic acid.
adiabatic
Adduct ions in an ESI spectrum
A term used in thermodynamics which describes an event in which no energy (heat) is transferred to or from the environment.
adiabatic ionisation Ionisation which takes place so rapidly that the newly formed ion remains in its lowest energy state, as occurs during electron ionisation.
aerosol A stable suspension of fine particles in a vapour, typically that formed in a pneumatically assisted electrospray ion source.
aerosol mass spectrometry The measurement of organic aerosol compositions in real time, generally by sampling at ambient pressure. Particle sizes are almost always determined at the same time and the technique has been applied to atmospheric aerosols, bioaerosols and aerosols from human breath.
affinity chromatography Liquid chromatography in which a particular compound or class of compounds is concentrated or purified by specific interaction with an immobilised ligand attached to the packed column stationary phase. The ligands include a wide variety of compounds but when antigens or antibodies are used the technique is often referred to as immunoaffinity chromatography. It is commonly used to purify biological molecules 7
algorithm from complex mixtures such as biofluids or peptide digests.
algorithm A software procedure in a computer program designed to perform a defined task. H2 C
H2 C
CH3
H3C O
H2 C
ε
alpha bond
H2 C
CH3
H3C O
Two bonds 'alpha' to the ionisation site.
Alpha bond
In discussing the fragmentation mechanism of an ion, the bond adjacent to the site of ionisation is frequently referred to as an alpha bond. In the ketone ionised by EI in the figure shown here, the arrows show the two alpha bonds.
alpha cleavage
Alpha cleavage
Fission of the alpha bond by a radical site-driven electron shift. Illustrated here for a ketone ionised by EI. Note the fishhook arrows designating single electron transfers.
alternating current (AC) An electrical current supply in which the magnitude and sign vary cyclically in the form of a sine wave.
ambient mass spectrometry A general term describing mass spectrometry in which ionisation takes place at ambient pressure and temperature, usually in the open air. Specific types include DESI and DART.
ammonia A gas, formula NH3, frequently used in CI sources to promote low-energy adduct ion formation. The most common species observed is the ammoniated adduct ion [M+NH4]+. The ionisation is softer than with methane or isobutane, the other two common CI gases. Ammonia is also used to moderate the electrons produced in negative-ion electron capture sources.
analogue ion Ions with similar chemical valence, such as [(CH3)2NC=S]+ and [(CH3)2NC=O]+.
8
analogue signal analogue signal A continuous electrical signal which is digitised prior to passing to a computerised data system. To be contrasted with pulse count signal acquisition. See also pulse count signal
analogue-to-digital converter (ADC) A device, usually based on a semiconductor chip, which samples an analogue signal, e.g. a voltage, and converts it into a digitised form. Important parameters include the number of bits that are output, the speed of conversion and the accuracy and precision. Virtually all signals from mass spectrometers are processed in this way prior to being passed to the data system. The inverse operation is performed by a DAC.
analyser That part of a mass spectrometer in which ions of differing m/z values are separated and ejected or are detected in situ. It can take the form of filters formed by parallel rods to which appropriate RF and DC voltages are applied (quadrupole filters), three-dimensional ion traps, again using RF and DC voltages (Paul trap or Orbitrap) or also with magnetic fields (Penning or ICR trap), magnetic and electrostatic fields (sector instruments) or time of flight arrangements. It is common for more than one analyser to be coupled together in tandem. See also tandem mass spectrometry
anchimeric assistance The participation of a neighbouring group in a molecule in the reaction of an adjacent part, resulting in an increase in the reaction rate. In MS, it is used to describe fragmentation mechanisms assisted in this manner. In the scheme here, the combined participation of the bromine radical loss and the formation of a stable ‘phenonium’ ion provide the driving force for this rearrangement.
Anchimeric assistance
anion Any atom, molecule, ion or fragment of a molecule carrying a negative charge.
anomeric configuration A term used in carbohydrate chemistry to define aspects of the stereochemistry of the molecule. 9
anti-aromatic ion anti-aromatic ion A planar cyclic ion containing alternating single and double bonds with a total of 4n π electrons (n = 0, 1, 2, 3 etc.) and it is therefore not aromatic.
antibody A large protein from the immunoglobulin family (IgA, IgD, IgE, IgG, IgM) which the immune system employs to recognise foreign molecules in the organism prior to their destruction and removal. Each immunoglobulin has two variable regions at the tips of the molecule that are designed specifically to bind to the target antigen. Antibody
antigen A foreign substance which elicits a response from the immune system. This molecule binds to the variable region of the antibody.
apparent mass The m/z value measured for metastable ions detected with double focussing magnetic analysers. The apparent mass is defined by the equation m* = m22/m1 where an ion of mass m1 produces a fragment with mass m2.
appearance energy In EI sources, the minimum electron energy at which an ion can be observed in the spectrum. Sometimes determined by the potential (volts) which is applied to the filament in an EI source relative to the source block.
appearance potential see appearance energy aptamer A synthetic small oligonucleotide or peptide molecule with an overall three-dimensional structure designed to bind strongly to a target molecule such as a protein, lipid or viral complex. Immobilised aptamers have been used to perform highly specific target molecule extraction and purification prior to MALDI-TOF MS. 10
argon argon An inert gas, symbol Ar, frequently used in lowenergy collision cells for tandem mass spectrometric experiments and to form the plasma in ICPMS experiments.
argon plasma Argon is used in ICPMS to form the ionising plasma as this has the advantage of forming multiply charged elemental ions, simplifying the resulting spectra.
aromatic ion A planar cyclic ion containing alternating single and double bonds with (4n + 2) electrons (n is a positive number representing the number of conjugated π electrons).
array detector
Argon plasma. Courtesy of Clarisse Mariet, CEA Saclay, France
A device in which a number of ion-detecting elements are arranged in a linear or twodimensional arrangement. This detector was designed to provide a modern digital version of the old photoplate detector with which an entire spectrum could be recorded without the need to mass scan a sector analyser.
associative ionisation A cooperative ionisation process in which two excited atoms or molecules react together to form a single adduct ion and an electron.
asymmetric field ion mobility spectrometry see high-field asymmetric waveform ion mobility spectrometry
Skimmers
Ions
Spray Needle/Capillary
Transfer capillary
Analyte/Solvent droplets (spray) Analyte/Eluent flow
To Mass Spectrometer
(syringe pump or LC) N2(g) flow
atmospheric pressure Atmospheric pressure varies with weather and altitude. Standard atmospheric pressure is defined as 1.01325 bar and 760 mm mercury or 760 Torr.
atmospheric pressure chemical ionisation (APCI) A form of API in which a high voltage applied to a fine needle produces a corona discharge in a heated spray of dissolved analyte, nitrogen gas and air. The plasma so formed contains solvent as well as oxygen and nitrogen radical ions which react with
Cone Nebulizer gas
Heater Corona dsicharge Pumping ATMOSPHERIC PRESSURE
Atmospheric pressure chemical ionisation (APCI). Reproduced from ‘Mass Spectrometry Ionisation Techniques and Applications for the Analysis of Organic Compounds’, P. J. Gates et al, in “Current Methods in Medicinal Chemistry and Biological Physics”, Carlton A. Taft and Carlos H. T. P. Silva, Research Signpost 2007, 81-308-0141-8
11
atmospheric pressure ionisation (API) traces of water to form H3O+ and OH- as well as other ions. These undergo ion/molecule reactions with the analyte to form [M+H]+ and [M-H]species. When employed in LC/MS, higher HPLC flow rates can be accepted than for ESI. Multiply charged species are not common. The abbreviation APcI is a commercial term.
atmospheric pressure ionisation (API) A general term for all forms of ionisation which can take place at atmospheric pressure including ESI, APCI, APPI and MALDI.
atmospheric pressure ion source Any ion source operating at atmospheric pressure.
atmospheric pressure MALDI MALDI can take place at AP, reduced pressure or in a high vacuum. The AP MALDI sources are easily interchanged with ESI or APCI ion sources. HPLC inlet Nebulizing gas
Nebulizer (sprayer) Vaporizer (heater)
Drying gas UV lamp hv
Capillary
© CHROMEDIA
Atmospheric pressure photoionisation (APPI), courtesy of Chromedia. This source is mounted in front of the entrance capillary to the mass spectrometer
atmospheric pressure photoionisation (APPI) A form of API in which the analyte is sprayed into the source, as in ESI and APCI sources, in a solvent frequently containing a dopant molecule such as toluene or acetone. The spray is irradiated by a powerful UV source that forms excited species which undergo secondary ion/radicalmolecule reactions with the analytes to cause ionisation. It is claimed to be the method of choice for detection of non-polar molecules in HPLC eluates. Protonated or deprotonated molecules or radical molecular ions can be formed, according to the mechanisms and thermodynamics involved.
atom gun A device designed to produce a collimated beam of energetic atoms from a heated source. In MS, this is the prime source for the formation of ions in a FAB source. Most SIMS and FAB sources use atom as well as ion guns, commonly with xenon atoms or caesium ions.
atomic mass The mass of an atom. The mass scale is a relative one based upon an agreed definition of the mass of an elemental isotope standard. Modern scales are 12
atomic mass unit (amu) based on the assumption that 12C has a mass of exactly 12.0000 and are expressed in unified atomic mass units.
atomic mass unit (amu) A term for atomic weight, originally based on the assumption of a mass of 16.0000 exactly for the 16 O isotope of oxygen. Now replaced by unified atomic mass unit (u). 1 u = 1 Da = 1.665 x 10-27 kg.
atomic weight A commonly used term for the average atomic weight of an element, calculated from the average of the constituent stable isotope masses of that element using the unified atomic mass scale. See average atomic weight
atto Abbreviation for 10-18. As in attomole.
autodetachment The spontaneous loss of an electron from an anion to produce a neutral species.
autoionisation The spontaneous loss of an electron from a neutral species via a radiationless transition from a discrete electronic level to an ionized continuum level of the same energy.
auxiliary gas An inert gas, usually nitrogen, added to an AP ion source to create an aerosol spray, to assist in solvent evaporation and to minimise access of the atmosphere to the source. Increased gas flow rates are required at higher solvent flows.
average atomic weight The average mass of an atom taking into account the masses of its constituent stable isotopes and their naturally occurring abundances using data on the unified atomic mass scale.
average molecular mass The mass of an ion or molecule calculated from the average atomic weights of the constituent isotopes and their natural abundances based on the unified atomic mass scale.
13
Avogadro number Avogadro number The number of atoms in 12 g, i.e. one mole, of 12 C. This is currently accepted as 6.02214199 x 1023.
axial ejection The application of a supplementary electric field to induce the ejection of ions from a trap.
axial oscillation Together with cyclotron and magnetron motion, a packet of ions in an ICR cell undergoes an oscillatory motion axial to the direction of the magnetic field. Also, for ions in an Orbitrap, a detection principle relies on the image current of the axial motion of ion packages orbiting the inner electrode. A diagram illustrating the axial and radial oscillations present in an Orbitrap. Courtesy of Thermo Scientific
14
axialisation The effect of retarding electric fields or of multiple collisions of ions and molecules to induce cooling and congregate the ions in a defined space, such as in an ion trap or an RF-only multipole element.
B
B B The symbol for a magnetic sector analyser.
B/E linked scan A linked scan at constant B/E in a sector mass spectrometer in which the magnetic field (B) and electric field (E) are scanned simultaneously while holding the accelerating voltage (V) constant, to maintain a constant value of B/E. This type of scan is used to record a product-ion spectrum.
bn ion An N-terminal ion formed by fission of a peptide ion at the C-N peptide bond. See peptide sequencing
background spectrum The mass spectrum that appears in the absence of a sample. This might be caused by residual gas species, or, in GC/MS and LC/MS systems, from column bleed or solvent impurities.
background-subtracted spectrum The mass spectrum of a sample obtained following 15
bar subtraction of the background spectrum recorded in the absence of sample.
bar A non-SI unit of pressure. One bar is equivalent to 14.5 psi, 760 mm mercury or 100,000 Pascal (the SI unit).
base peak
Background-subtracted spectrum. The lower panel shows the unaltered spectrum and the upper the result after subtracting an average set of spectra acquired before and after the detected peak from an average of the latter’s spectra
The most intense ion in a mass spectrum. The abundance of this ion is used as the base from which to normalise the relative abundances of the remaining peaks in the spectrum and is given a nominal value of 100%.
basic residue An amino acid residue in a peptide or protein that has a basic nature, such as arginine, histidine and lysine.
Bayard-Alpert ion gauge A hot cathode ion gauge for measuring the pressure of a residual gas. The electrons from a filament are accelerated towards an anode and collide with the gas molecules, producing cations which are measured by an ion detector. The current flowing is directly proportional to the residual gas pressure. This type of gauge indicates the pressure from 10-1 to 10-8 Torr.
benzylic cleavage Bayard-Alpert ion gauge. Photograph by Tony Mallet
A beta-fragmentation as shown in the figure, occurring at the carbon atom adjacent to a phenyl group, resulting in a benzyl or substituted benzyl ion.
Bessel box
Benzylic cleavage
An energy focussing filter designed to remove low-energy and high-energy ions and permit the passage of a set of ions of intermediate energy. Combined with a quadrupole mass spectrometer, it can be used to perform ion energy analysis.
beta-cleavage Fission of a bond two removed from a heteroatom or functional group, producing a radical and an ion. Also written as β-cleavage. Beta-cleavage
16
binding energy binding energy The energy required to separate particles bound together by nuclear or electromagnetic forces, such as electrons and protons.
bioaerosol An aerosol consisting of living microorganisms such as fungi, bacteria or viruses.
bioinformatics The application of information science to biology, using statistical and mathematical techniques to solve biological problems such as protein structure and function prediction, protein interactions and genome and proteome sequencing.
biomarker A compound produced by a system that is predictive for a particular condition, or the presence of certain other compounds. Biomarkers are used, for example, in disease diagnostics, for detecting drugs and in petroleum exploration.
biomolecular interaction analysis (BIA) A technique, commercially implemented, for characterising interactions between biomolecules, using a biosensor that employs surface plasmon resonance. The biosensor comprises a specific compound immobilised on a surface, which selectively interacts with different compounds in the sample. BIA is used typically to study binding strengths, kinetics of reaction, concentrations and complex formation between different biomolecules. Interactions between proteins (including antibodies, enzymes and receptors), peptides, nucleotides, carbohydrates and small molecules can be studied.
biomolecule A compound that occurs naturally in a biological system. It can be a small molecule (sugar, lipid, sterol, amino acid, nucleoside, nucleotide, peptide) or a large molecule (protein, enzyme, polysaccharide, DNA, RNA).
17
biopolymer biopolymer A polymer that occurs naturally in a biological system, including polypeptides, proteins, DNA, RNA and oligosaccharides.
blackbody infrared radiative dissociation (BIRD) A method for fragmenting ions for tandem MS that uses blackbody irradiation to excite and dissociate the ions. The radiation is usually generated by heating the vacuum chamber walls. The technique is most commonly used in FTICR MS.
Boltzmann distribution An expression that predicts the proportion of particles that exist in a particular energy state, that is, at a certain temperature. It is described by the equation: P(E) = Aexp(−E/(kT))
A plot of the distribution of the numbers of molecules against their kinetic energies
where P(E) is the probability that a particle has energy E, A is a constant, T is the temperature and k is the Boltzmann constant. This distribution of energies is illustrated in the figure.
Boltzmann’s constant A constant (symbol k) relating the absolute temperature to the kinetic energy of a molecule in an ideal gas. It is defined by the relationship PV = NkT where P = pressure, V = volume, N is the total number of molecules in the gas and T is temperature. It has a value of 1.3806505 x 10-23 J K-1.
bond dissociation energy Also referred to as bond energy, it is the enthalpy change in breaking a single bond in a neutral molecule. Thus, the bond energy of a single C-H bond in methane is 435 kJ/mole. Bond energies in ionised molecules can differ from those in uncharged species.
bond resonance Bond resonance is possible whenever a Lewis 18
bottom-up protein identification structure has a multiple bond and an adjacent atom with at least one lone pair of electrons. In the diagram here, neither of the bonds is fixed as single or double but each is identical with a character in between these extreme canonical structures.
Bond resonance in an acetate ion
bottom-up protein identification Single purified proteins are proteolytically digested and the resulting peptides are sequenced by tandem MS. The most likely identity of the parent protein is deduced by reference to published protein databases.
Bradbury Neilson ion gate A set of fine wire grids with applied varying potentials designed to control the passage of electrons, this device is used in TOF analysers to control and select the passage of ions of defined flight time, or m/z value. The figure illustrates the effect on an ion beam of applied potentials to the wires.
broadband excitation The application of an additional RF frequency sweep signal to a set of trapped ions whereby extra kinetic energy is applied and ion decomposition occurs through collision with inert gas. See chirp
Bradbury Neilson ion gate
buffer gas The inert gas that is added to an ion trap to reduce the kinetic energy of the ions present by collisional deactivation. This prevents them from dispersing spatially, focussing them into a small central volume. The term is also used for the gas added to ion traps or collision cells to bring about CID. Common buffer gases are helium, xenon and nitrogen.
19
cn ion
C cn ion An N-terminal ion formed by fission of a peptide ion at the N-C peptide bond. See peptide sequencing
CAD-MIKES see mass-analysed ion kinetic energy spectrometry (MIKES) caesium A metallic element, symbol Cs and atomic number 55, salts of which are used in an atom gun to produce a beam of Cs atoms and ions as projectiles in a FAB source. CsI is also used in the calibration of mass spectrometers with FAB and API sources as it provides numerous cluster ion signals over a wide m/z range.
calibration The majority of mass spectrometers will record the intensity of ion current as a function of time, when set to scan a mass spectrum. It is necessary to carry out a mass calibration experiment by which the time parameter is converted to an m/z value. A conversion table for this is stored in the computer 20
calibration compound and modern data systems will perform this operation on the fly. Creation of this table is the calibration process and it has to be repeated at varying intervals according to the nature and stability of the analyser and the degree of accuracy required.
calibration compound A substance or mixture of compounds which provides a sufficient number of ions of known, accurate, m/z value to cover the desired mass range of the analysis to be performed. A table of the m/z values is saved in the data system and is employed to create a look-up table for the conversion of the time of signal arrival actually determined by the instrument. The number of calibration ions required depends on the analyser: a scanned magnet requires a regular series throughout the mass range while a TOF analyser may only need a few ions.
californium
252
Cf desorption
A technique for the desorption and ionisation of condensed phase analytes by bombardment with the alpha particles emitted from a radioactive 252Cf source. The sample is coated on a thin foil and the 252 Cf source is placed behind it. The fission fragments penetrate the foil and desorb ions from the sample. A TOF mass analyser is employed in conjunction with this ion source as the emission of the radioactive particle is accompanied by a simultaneous emission of another particle 180° in the opposite direction. This latter provides the ‘start’ signal for the TOF measurement. The technique suffers from low sensitivity and has been superseded by MALDI-TOF MS.
Californium 252Cf desorption. Diagram of 252 Cf-PDMS time of flight mass spectrometer. Ions emerging from the sample foil are accelerated through the grid assembly and into a field-free region shielded by a Faraday cage. The main section of the flight tube contains an axial electrostatic field to increase ion transmission
capillary column A chromatography column with an internal diameter in the region of 50 to 500 μm. For GC, columns are made of flexible silica tubing up to 100 m in length, coated externally in a nylon film to provide mechanical strength and internally with a liquid stationary phase. Packed capillary columns with internal diameters of 350 to 50 μm are also employed in micro/nano HPLC applications.
The forte™ capillary column, courtesy of SGE
21
capillary electrophoresis (CE) capillary electrophoresis (CE) Electrophoretic separation performed in a buffer solution held in a length of silica capillary tubing. This configuration leads to very narrow peak widths and the dimensions of the tubing permit efficient cooling when high voltages are applied. The technique couples easily to a mass spectrometer with a low flow API ion source such as electrospray. The narrow peak widths require a fast scanning mass analyser.
cation Any atom, molecule, ion or fragment of a molecule carrying a positive charge.
cationisation The non-covalent attachment of a positively charged species to a neutral molecule; typically the addition of Na+ to form an ion [M + Na]+ in API.
cationised molecule An ion formed by the non-covalent attachment of a cation to a neutral molecule.
centi One hundredth part, e.g. centilitre.
centroid The centre of gravity of a detected peak. This parameter is used to determine the m/z of the detected ion and produce a centroided (‘stick’) spectrum. The figure shows a symmetrical ion signal peak and the position of the centroid. A plot of m/z versus ion intensity showing the centre of gravity or centroid S6 241007RC02 80 (1.359) Cn (Cen,2, 80.00, Ht); Sm (Mn, 2x0.70); Cm (76:86) 100
Scan ES+
267.4 1.32e8
226.3
Centroided Spectrum % 170.1 211.2
176.1
184.9
192.1
199.1
208.1
0 241007RC02 80 (1.359) Sm (Mn, 2x0.70); Cm (76:86) 100
215.2 220.2
233.2
242.3
253.3
264.3
Scan ES+
267.4 1.33e8 226.3
Continuum Spectrum % 170.1 211.2 192.1
0
170
180
190
242.3
199.1
200
210
Centroided spectrum
220
230
240
250
260
270
m/z
centroided spectrum The complete data set for a spectrum contains a large matrix of time or m/z measurements versus ion intensities. This can be simplified to a compact form by thresholding the signal, calculating the centroid of each peak and plotting the two-piece data set of time or m/z at the centroid position versus the maximum intensity of the signal. Sometimes referred to as a ‘stick’ spectrum. The figure shows a continuum spectrum (lower panel) and the corresponding centroided spectrum (upper panel).
certified reference material (CRM) A reference material for which certain properties 22
channel electron multiplier have been certified at a stated level of confidence. They are used in MS in quantitative studies, where the concentrations of certain compounds in the material have been certified.
channel electron multiplier see continuous dynode electron multiplier charge The positive or negative electrical charge sited on a specific atom in a cation or anion.
charge delocalisation A term to describe the extent to which a charge is confined to one site on a molecule or is distributed throughout the molecule. These differences will significantly influence the CID of molecules such as lipids and peptides.
charge derivatisation A chemical reaction to introduce a fixed charge into a molecule. For example, aldehydes and ketones can be derivatised with Girard’s T reagent as shown in the figure, to introduce a positive charge on the molecule.
charge exchange The transfer of a charge from an ion to a neutral species as a consequence of a collision. Frequently observed for ions formed by high-energy collisions and in ionisation by the dopant in APPI.
Charge derivatisation of an aldehyde
charge-induced fragmentation see heterolytic fragmentation charge inversion A reaction between an ion and a neutral species which leads to the reversal of the charge on the ion. With sufficient collision energy, electrons can be stripped off the ion leading to a change in the sign of the charge. This is shown in the figure.
Charge inversion
charge localisation The fixing of the charge on a defined point in a molecule.
charge migration Fragmentation of an even-electron ion in which 23
charge number (z) the charge transfers to another atom on the structure.
charge number (z) The number of positive or negative charges residing on the ion.
charge on the electron 1.602177 x 10-19 Coulombs
charge-remote fragmentation
The charge-remote fragmentation of 12hydroxy stearic acid
This term is used for an even-electron ion where bond breaking takes place at a site distant from the initial charge position. Thus, in the molecule shown in the figure here, charge-induced fragmentation is observed adjacent to the hydroxyl groups arising from the charge on the acid anion.
charge residue model One theoretical treatment of the formation of ions in an ESI source (see also ion evaporation model) in which, as each charged droplet reaches the Rayleigh limit, a succession of droplets of ever diminishing size is formed until a charged molecule is left on its own in the gas phase.
charge retention Ion fragmentation in which the initial charge is retained on the original site. An example can be found in the case of CID of a molecule which can be cationised in an ESI source both by protonation and by alkali metal cationisation. The former is mobile and can lead to fragmentation directed from a number of charge sites while the latter tends to remain fixed on one part of the molecule and will show different and fewer product ions
charge stripping A process in which collisional activation at high energies is used to remove one or more electrons from a cation or anion, thus changing the number of charges on the species and even causing charge inversion. See accelerator mass spectrometry and electron transfer dissociation
24
chelate chelate A complex containing, typically, a central metal ion to which are attached one or more organic molecules with bonds to the metal ion at two or more loci.
chemical ionisation (CI) Ionisation by the addition of a charged species to a neutral molecule or by removal of a proton. The product ion is an even-electron ion with low internal energy and undergoes little fragmentation. The initial reaction can take place in vacuum in an EI source containing relatively high pressures of gases such as ammonia or methane, or in an APCI source where the reactant ions are provided by a plasma created by a corona discharge. The figure shows a CI source insert.
Mn+
Chelate
chemical libraries Collections of synthetic substances usually in the context of candidates created for drug discovery. These can amount to several million items and automated MS is routinely used to determine the stability and purity of these collections.
chemical noise Background signals observed in the mass spectrum originating either from the presence of impurities in the sample or in the sample matrix, or from the presence of extraneous compounds in the absence of analyte.
chemical reaction interface mass spectrometry (CRIMS)
A plug-in CI source for a bench-top GCMS instrument. Photograph by Tony Mallet
A technique in which compounds eluting from a chromatographic system are reacted with a reagent gas in a microwave cavity to form low-molecularweight species which can be analysed by MS. In the case of a component separated by HPLC, the solvent is removed by a particle beam interface and the analytes are reacted with a reagent gas.
chemi-ionisation The reaction of a molecule with an internally excited atom or molecule to form an ion. Distinguished from CI. A schematic for an HPLC/CRIMS Instrument. F.P. Abrahamson in J. Chromatog. A 1996 732 1899
25
chemometrics chemometrics Mathematical, statistical, graphical or symbolic methods to improve the understanding of chemical information. These include techniques for the effective statistical analysis of experiments in which large amounts of data are accumulated with multiple variables.
chiral Chiral organic compounds contain a carbon atom with four distinct groups attached as shown in the figure. They are asymmetric and optically active. See also stereochemistry
chirp A term used in FTICR MS to describe broadband ion cyclotron excitation using a frequency sweep by which the trapped ion packet is moved outwards to circulate closer to the detection electrodes.
chopper amplifier A semiconductor device designed to induce as little noise as possible while converting a DC signal input into a square-wave AC signal output with the aid of one or more choppers.
chromatography A collection of methods for the separation of mixtures of compounds. They all have in common the creation of a two-phase system, one of which is fixed and designed to differentially attract compounds and the other is moving and arranged to elute substances. The two phases are kept in intimate contact and different substances partition differentially between the two.
classical ion A tricoordinated carbenium ion, such as C2H5+, as opposed to the non-classical hypervalent carbonium ion such as CH5+.
closed-shell An alternative term for a molecule with paired electrons.
cluster formation The formation of aggregates of molecules and 26
coherent radiation ions, especially prevalent in AP ion sources where adiabatic expansion into a vacuum causes strong cooling of the droplets. The effect is minimised by the application of heat to the source and collision with flows of an inert gas.
coherent radiation Electromagnetic radiation that is in phase, so that the waves travel in unison, as in a laser producing coherent light.
collector This term has been used to describe the Faraday cup ion detector installed in a stable isotope ratio mass spectrometer
collimating Literally to ‘make parallel’; thus collimating magnets are used in an EI source to focus the beam of electrons from the filament into a narrow beam. Collimating slits are used to constrain an ion beam in a similar manner.
collisional activation Kinetic energy transfer to an ion by collision with a neutral molecule or a surface.
collisional focussing In the quadrupole ion trap, ions are focussed towards the centre of the trap by collisional cooling with helium ions, where focussing forces are balanced by space charge. Ions with the lowest mass-to charge ratios are nearest the centre, with ions of higher mass arranged further out in layers, like the rings of an onion. These ions can be stored for long periods, providing improvements in mass selectivity and axial ejection, and enhancing process such as laser dissociation, since the ion cloud is more easily irradiated. Collisional focussing can also be carried out in other traps and focussing devices such as wave guides and hexapoles.
collisionally activated dissociation (CAD) see collision-induced dissociation collision cell A region of relatively higher pressure placed after
Collision Cell with cutaway showing Hexapole rods used in the Thermo Scientific XSERIES 2 ICPMS. (Image supplied by Thermo Fisher Scientific).
27
collision gas the first analyser in an MS/MS instrument for the CID of precursor ions. It is usually a multipole rod transmission device to which appropriate RF voltages are applied to assist in focussing the ions present. See also collision reaction cell
50% 40% 30%
collision gas An inert gas introduced at a relatively high pressure into a collision cell to promote decomposition of the precursor ion.
collision, high-energy In practice, this term is used for CID experiments in which the energies involved are in the keV range. These are typical of tandem MS with instruments having magnetic or TOF analysers and usually involve single collisions.
30 msec Diagram of Stepped Normalized Collision Energy Activation, a method to improve product ion formation in an ion trap. Courtesy of Thermo Scientific
α-Naphthylred
Neocuproine
Triamterene
collision-induced dissociation (CID)
Ellipticene
76.90 209.02
247.09
237.06
254.09
232.11 104.84
232.00 143.00 220.03
100
150 m/z
212.03
200
250
50
100
150
200
50
100
m/z
α-Naphthylred
Neocuproine
150 m/z
200
181.03
100
150 m/z
200
250
Ellipticene
76.87
164.85
250
Triamterene
232.1
237.00
193.05
247.2
206.99
The fragmentation of an ion by collision with an inert gas or neutral molecule or with a surface. The event is usually designed to take place at controlled energies in a collision cell with a specifically chosen precursor ion giving rise to one or more product ions. Also referred to as collisionally activated dissociation (CAD). See also surface-induced dissociation
231.99 104.93 108.93
143.01
100
150 m/z
220.01
245.99
200
250
138.96 211.97
50
100
150 m/z
200
50
100
150 m/z
200
121.0 250
100
191.3 150 m/z
200
250
Fragmentation of α-naphthyl red, neocuproine, ellipticene and triamterene with 40% Normalized Collision Energy NCE (top) and with Stepped Normalized Collision Energy (SNCE), 40% midpoint, 20% range and three steps (bottom) – Courtesy of Thermo Scientific
collision, low-energy Collisional energies in the 0 to 100 eV range which are common in tandem MS performed with traps and quadrupole analysers. Multiple collisions are common in these experiments.
collision reaction cell In an ICPMS instrument, a collision cell is used to minimise isobaric interference ions by charge exchange neutralisation.
column bleed The normal background signal issuing from the chromatography column that reaches the detector in the absence of analyte. It results from the breakdown of the stationary phase. In practice, the total signal reaching the detector is often attributed to column bleed but it may also contain signals from the injector, detector and other components.
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competitive ionisation competitive ionisation The ionisation efficiencies of different molecules can differ significantly and, when more than one species is present in the source, the ionisation of one molecule can suppress that of others present at the same time. A consequence of this is that, without separation and calibration, MS is not always a reliable way to determine the composition of mixtures. See also matrix effects
computer acquisition The size and rate of formation of the data set from a mass spectrometer experiment precludes any non-computerised acquisition method. The raw data signals have to be digitised, thresholded and processed, the signal peaks centroided and the data presented in the form of real-time chromatograms and spectra. Increasingly common is the use of computerised analysis of the data produced, in real-time, to control the experiments being performed.
concentration The amount of a substance in a given volume of solvent. Units can be weight per volume or molarity.
concentration-dependent detection Some ionisation processes are dependent on the concentration of the sample being introduced whereas others depend on the mass flow of material. ESI is concentration dependent except at low flow rates, while APCI is mass flow dependent. See also mass-flow-dependent detection
conductance The ratio of throughput to the pressure differential between two specified isobaric sections inside the pumping system, under steady-state conservation conditions. It is used to calculate the pumping speed of the system.
cone A conical stainless steel device with a fine hole in the apex, present in some makes of instrument, designed to transmit ions from AP into a differentially pumped interface region, while maintaining the pressure differential between the
A metal cone with a fine aperture in the apex from an early API mass spectrometer. Photograph by Tony Mallet
29
cone gas two regions. Other instruments use a length of capillary tubing.
cone gas A flow of inert gas, usually nitrogen, over the fine aperture through which ions formed at AP pass into the vacuum of the mass spectrometer. It is designed to assist in reducing the formation of clusters and adduct ions and keep the sample cone clean.
cone voltage A low voltage differential is maintained between an API source cone or entrance capillary and the body of the mass spectrometer to direct ions into the analyser. At this stage, the ions are present in a relatively high pressure region and collide frequently with residual air, solvent etc. If this voltage is raised sufficiently, CID fragmentation can take place and product ions can be detected. In instruments with no cone a similar procedure is referred to as ‘in-source fragmentation’
consecutive reaction monitoring Use of an MSn multi-step ion experiment with more than two stages of ion fragmentation and separation, to monitor specifically the precursor and final generation product ion pairs in a multistep fragmentation pathway. It is most often used to analyse GC and LC effluents and is limited to ion traps.
constant neutral loss scan (CNL) A tandem MS scan in which both analysers are scanned over the defined m/z range but with a constant mass offset maintained between the two scan laws. All ions which undergo the same m/z loss on CID will be detected. Thus, this mode can be used to detect all ions losing, say a methyl radical, or water, or all precursor ions from which the common ion can arise. Strictly, this mode of scan cannot be performed in a trap instrument. Also known as constant neutral mass loss scan and fixed neutral fragment scan.
constant neutral mass gain scan A tandem MS scan in which both analysers are scanned over the defined m/z range but with a constant mass offset maintained between the two 30
continuous dynode electron multiplier scan laws. All ions which undergo the same m/z change on CID will be detected. It is used with ion/molecule reactions to detect all ions gaining, say, a molecule of water, or all precursor ions for which a common gain occurs.
continuous dynode electron multiplier An electron multiplier shaped like a horn with a continuous reactive internal surface. The impact of one electron in the entrance will lead to an increasing cascade of electrons as the particles reflect from one side of the horn to the other. Also known as a channel electron multiplier.
continuous-flow fast atom bombardment A method for interfacing a low-flow capillary HPLC separation to a FAB probe. The solvent, containing FAB matrix, is allowed to flow into the high vacuum of the FAB source and emerges through a stainless steel frit surrounded by a fabric from which excess solvent is vaporised smoothly. The FAB gun is focussed on the frit to ionise analytes in the solvent-matrix stream. This technique has been superseded by modern AP sources.
A CF-FAB probe from a magnetic sector instrument (VG 7070SE). Photograph by Tony Mallet
continuum mode see profile mode continuum spectrum see profile mode spectrum conversion dynode A metal surface at a high potential on to which ions collide after leaving the analyser. A stream of secondary electrons is produced and these are detected by electron multiplier or photomultiplier detectors.
cooling In MS, this usually refers to the removal of energy, both translational and internal, from newly formed ions. It is often achieved during collision with an inert neutral atom or molecule at a relatively high pressure. Careful attention to this aspect of ion formation is essential in a number of cases, e.g. the preservation of the full three-dimensional structure of large biological non-covalent complexes such as proteasomes and also in maintaining a packet of ions in a closely defined space in a trap. 31
corona discharge corona discharge If a sharp point with a high voltage is present in the atmosphere or in the presence of solvent, a discharge is observed due to the formation of an electrically conducting plasma. This contains ions and radicals arising principally from the ionisation of nitrogen and water. In MS, a corona discharge is used to effect ionisation in APCI.
Coulomb The SI unit of electrical charge, being the quantity of electricity carried by a current of one ampere for one second
Coulombic forces The mutual attraction between charges of opposite sign leads to non-covalent aggregations which can be analysed by soft ionisation methods such as ESI.
Coulomb repulsion The mutual repulsion between two or more ions of identical charge sign.
cryogenic The use of low temperatures, usually associated with liquid helium.
cryogenic detector A detector operating at temperatures in the sub 1 K level. This is a semiconductor device which, at very low temperatures, is able to detect the impact of an ion on a surface. Used in the detection of large-mass ions produced by MALDI sources and analysed by TOF analysers as there is no discrimination against high-mass ions. See superconducting tunnel junction detector
cryogenic pump A vacuum pump which operates by condensing out all gases present onto a liquid helium-cooled surface.
curtain gas
Cryogenic pump. Courtesy of Oxford Instruments
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The inert gas flow, usually nitrogen, into an AP ion source which acts to de-cluster the newly formed ions, drive solvents and buffers from the inlet, and to prevent ambient air entering the mass spectrometer.
curved field reflectron curved field reflectron A TOF reflectron in which a non-linear retarding field is created. The diagram illustrates one implementation of this. This has the advantage that PSD spectra can be recorded without stitching several m/z ranges together and is central to the performance of a TOF-TOF instrument.
cyclotron frequency The frequency of the angular motion of an ion in an ICR cell subjected to a magnetic field. For a fixed magnetic field strength this frequency depends only on the m/z of the ion. The range of frequencies observed for a magnetic field strength of 9 Tesla and for ions up to 200,000 m/z is in the kHz to MHz range. The radius of motion is inversely proportional to the magnetic field and increases with m/z of the ion.
cyclotron motion An ion is constrained to move in a circular path in a plane at right angles to the direction of a strong magnetic field.
Curved field reflectron. Reproduced with permission from ‘A Curved Field Reflectron Time-of-Flight Mass Spectrometer for the Simultaneous Focusing of Metastable Product Ions’ by T.J. Cornish and R. J. Cotter, Rapid Communications in Mass Spectrometry, 8, 781-785 (1994) © John Wiley & Sons, Ltd
v
B +
−
qv × B
v
qv × B
The circular motion of an ion in a magnetic field applied in a perpendicular direction to the plane of the paper. Cations and anions move in opposite directions
33
dalton
D dalton A non-SI unit of mass, symbol Da, equal to the unified atomic mass unit (symbol u). It is defined as one-twelfth of the mass of one atom of carbon12, following the convention that an atom of carbon-12 has exactly 12 atomic mass units (amu). The value of the dalton is 1.66053886 x 10-27 kg. The dalton should not be confused with m/z, which is the ratio of mass to the number of charges on an ion.
Daly detector
A Daly detector from a VG 7070SE magnetic instrument. Photograph by Tony Mallet
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Ions exiting from the analyser are made to impact on a conversion dynode, thus releasing a stream of electrons. These fall on a phosphor screen, releasing photons which are subsequently detected by a photomultiplier. By switching the polarity of the dynode, both positive and negative ions can be detected efficiently. This arrangement has the advantage over a single electron multiplier that it is kept in a sealed environment.
dark noise dark noise The background signal from a detector in the absence of an instrument response to a sample.
data acquisition The process of converting the MS signals into a form that can be used. The signals can be acquired in one of several modes, including full scanning, selected ion monitoring and selected reaction monitoring.
database A collection of records in a particular subject area, such as thermodynamic quantities, mass spectra, retention indices, peptide masses and sequences, or protein structures. In proteomics the existence of DNA/RNA/Genome/Protein databases is a prime factor in successful protein identification.
Neutral loss scan. Flow chart for datadependent™ constant neutral loss (DDCNL) scan events Data. Courtesy of Thermo Scientific
data-dependent acquisition The acquisition of data after particular conditions have been met in a mass spectrum. For peptide mixtures, data-dependent MS/MS spectra are recorded in real time for the n most intense ions in a mass spectrum, where n is defined by the analyst. In other cases, spectra are recorded when the intensity of a particular ion signal exceeds a threshold value.
data processing A term for any kind of data analysis in which the data from the MS detector is manipulated to produce results. This is generally carried out by automated procedures and includes such operations as thresholding, peak centroiding, noise reduction, peak finding and deconvolution.
Ion trap. llustration of Multistage Activation and data dependent neutral loss MS3 (DDNLMS3) approaches using ion trap mass spectrometry. Courtesy of Thermo Scientific
data system The computer and software for processing data acquired by MS. Many operations are set to occur automatically and others can be controlled by the analyst.
daughter ion A secondary ion produced in an MS/MS spectrum by fragmentation of the precursor ion (parent ion) generally by CID, absorption of a photon, unimolecular decomposition or by modification of 35
daughter-ion scan the total number of charges. Although still in common use, gender-specific terms such as these are regarded by some as inappropriate and the daughter ion is referred to as the product ion.
daughter-ion scan A scan in which the product ions formed from a precursor (or parent) ion, generally by CID, absorption of a photon, or unimolecular decomposition, are recorded. Although it is still in common use, this gender-specific term is now regarded by some as inappropriate and is usually referred to as the product-ion scan.
DC discharge An electrical discharge produced by passing DC through an ionised gas. In MS, it is used for GDMS.
dead time The time after acceptance of a detected ion before a subsequent ion can be detected.
deca Prefix meaning ten, as in decabromodiphenyl ether.
decade An order of magnitude change in m/z value scanned by magnetic sectors and double focussing instruments, such as m/z 50-500.
deci One tenth part, as in decilitre.
deconvoluted mass spectrum This has several meanings within MS. 1. Charge deconvolution refers to the processing of a mass spectrum of multiply charged ions to determine the molecular mass of the original molecule. It is used particularly for protein analysis. 2. Deconvolution also refers to the extraction of spectra of individual components from those of coeluting species in a chromatogram. Algorithms have been written to achieve this, including AMDIS (Automated Mass Spectral Deconvolution and Identification System) from the National Institute of Standards and Technology and 36
defocussing voltage scan proprietary routines from instrument manufacturers. 3. Deconvolution is also used to describe the separation of overlapping peaks derived from the mass spectra of peptides in mixtures, in which the isotope peaks are resolved. Appropriate software is used to extract the mass spectra of the individual peptides. 4. Spectra containing multiply and single charged ions can be deconvoluted to show only the singly charged species. The figure shows the original ESI spectrum (upper panel) and the simplified spectrum (lower panel).
Deconvoluted mass spectrum
defocussing voltage scan An ion that fragments between the source and the first analyser in a sector instrument is not detected because its velocity is the same as that of its precursor ion. In a defocussing voltage scan, the precursor ion is accelerated, before its fragmentation, to a velocity equal to that required to focus the product ion, allowing the product ion to be detected. This scan permits the detection of all precursors of a given fragment. This mode is effective for small mass ranges where a rapid scan rate is required but cannot be used for a wide m/z range as the drop in accelerating voltage leads to defocussing of the instrument. See also accelerating voltage scan.
delayed extraction A technique in TOF MS in which improved resolution is obtained by applying a controlled delay between ion formation and acceleration. Also referred to as pulsed ion extraction or timelag focussing. The process is illustrated in the figure.
A delayed extraction MALDI TOF source. The initial population of ions is extracted in a two-stage process. The ions intitially formed with high kinetic energy move further away from the source electrode and therefore take up less energy from the second 6 kV pulse. If correct times and voltage are applied all ions of the same m/z will arrive at the detector simultaneously
delocalisation A concept used to describe π bonding in a conjugated system, in which the electrons are not localised between two atoms but extend over two or more adjacent atoms. The resultant bonds have a fractional double bond character. Delocalisation is found in aromatic systems and conjugated π bonded systems. The figure shows delocalised π bonding in a benzene ring.
Delocalisation in a benzene ring
37
delta permil delta permil The notation for describing stable isotope compositions of elements of low abundance, which stands for delta value in parts per thousand. It is determined relative to a standard of known composition, using the formula below, where R is the ratio of the heavy to light isotope. delta permil = (Rsample/Rstandard - 1)/1000 delta permil is represented as δ‰ and is spelled out several ways, including per mil, permil, per mill and per mille.
deprotonated molecular ion The negative ion formed by loss of a proton (H+) from the intact molecule. Although in common use, this term is strictly incorrect because it implies that the molecular ion, which is charged, has lost a proton. A more correct term for this anion is a deprotonated molecule.
derivatisation
Derivitisation of an alcohol to a silyl ether
A chemical reaction which is used to change the properties of the analyte and make it more amenable to MS. A common derivatisation reaction in GC/MS is silylation, in which polar hydroxy and carboxy groups are converted to silyl derivatives to increase their volatility but the derivatives must also be thermally stable. Other derivatisations are carried out to generate more informative mass spectra, or to introduce charge into the molecule (charge derivatisation).
desolvation gas see drying gas desorption chemical ionisation (DCI) A form of CI particularly for non-volatile compounds in which the non-volatile analyte is deposited on a filament that is subsequently heated rapidly by the passage of an electric current. The analyte molecules are desorbed and undergo ion/molecule reactions with ions produced from a reagent gas to form analyte ions for analysis. Typical reagent gases are methane and other simple alkanes.
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desorption electron ionisation (DEI) desorption electron ionisation (DEI) A form of electron ionisation in which the analyte is deposited on a filament that is subsequently heated rapidly by the passage of an electric current. The analyte molecules are desorbed and pass through an electron beam that induces ionisation.
desorption electrospray ionisation (DESI) An ionisation technique that takes place outside of the mass spectrometer, at ambient temperature and pressure. A fine spray of charged droplets, formed by pneumatically assisted electrospray ionisation at high potential, typically 2-5 kV, is directed towards the sample on a surface. Ions produced from the sample are drawn into the mass spectrometer via a vacuum interface. Most surfaces and analytes are amenable and no sample preparation or pre-separation is required. Analytes may be analysed in situ, such as explosives on luggage, drugs in urine and metabolites in tissue.
desorption ionisation The general term for the desorption and ionisation of analytes from surfaces, which includes DCI, DEI, DESI, DIOS, FAB, LDI, MALDI and 242Cf.
Desorption electrospray ionisation (DESI). An Omni Spray® Ion Source on a Waters LCT Premier mass spectrometer, Courtesy of Proslia Inc.
desorption/ionisation on silicon (DIOS) An ionisation technique in which samples are deposited on a porous silicon surface, in the absence of matrix, and subjected to laser desorption/ionisation. The technique does not suffer from interfering, matrix-generated peaks and yields little or no fragmentation, allowing molecular ions to be detected. It is applicable to both solid and liquid analytes.
detection limit see limit of detection detector A device that detects the ions produced in the mass spectrometer and produces a measurable signal, generally an electronic signal. In most detectors, this signal is amplified. Common types include the Faraday cup, the electron multiplier, the microchannel plate detector and the Daly photomultiplier detector.
Desorption/ionisation on silicon (DIOS). Courtesy of Dr M.G. Finn and Dr G. Siuzdak, The Scripps Research Institute, La Jolla, CA, USA
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detector response detector response Detector response can be described in two ways. It can be defined as the signal output for unit change in solute concentration flowing through the instrument, as is the case for an ESI source, or, for a mass sensitive detector, the voltage output for unit change in solute mass passing through the detector as is found in a GC flame ionisation detector.
deuterium The isotope of hydrogen, symbol D or 2H, with several uses in MS. It is used for labelling compounds to help elucidate reaction mechanisms and fragmentation mechanisms. Deuteriumlabelled internal standards are used in quantitative studies and, in conjunction with the corresponding non-labelled compounds, as derivatising agents for labelling in quantitative peptidomics and proteomics. Proteins are labelled with deuterium or studied in deuterium-substituted solvents in order to study their three-dimensional folding. See also hydrogen/deuterium exchange
diagnostic ion A characteristic fragment ion in a mass spectrum which is indicative of a particular structural group in its precursor. For instance, the appearance of the tropylium ion at m/z 91, usually indicates the presence of a benzyl group.
diaphragm gauge A pressure gauge for measuring small pressure differences, comprising a diaphragm that separates the pressure being measured from atmospheric pressure. The diaphragm is connected to a pointer via a spring and any pressure changes move the diaphragm upwards or downwards, to change the position of the pointer.
diaphragm vacuum pump
Diaphragm gauge. Courtesy of INFICON Limited, Liechtenstein
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A single-stage or multistage dry compressing vacuum pump that is oil free. A tensioned diaphragm is moved in an oscillating manner, increasing and decreasing the volume of the pumping chamber to produce the pumping action.
dication dication A doubly-charged ion formed by the loss of two electrons from a neutral species, such as Ca2+ or [C24H12]2+.
dielectric barrier discharge ionisation (DBDI) A form of ambient ionisation in which a discharge electrode is positioned above a glass slide placed on top of a copper sheet electrode. The slide acts as the sample plate as well as a dielectric barrier. A stable, low-temperature plasma is formed between the discharge electrode and the slide to desorb and ionise the analytes.
differential mobility spectrometry (DMS) see high-field asymmetric waveform ion mobility spectrometry differential pumping Adjacent and connected regions of the mass spectrometer, such as the ion source and the mass analyser, or the analyser and a collision chamber, may have different pressure requirements. For example, the ion source in API is at AP and that in a GC/MS system can be in the range from 0.1-100 Pa, but the analyser is at much lower pressure in both cases. The problem is circumvented by having independent pumping systems, with different pumping capacities, for the two regions or using a single pump with different conductances for the two parts.
diffusion pump A high vacuum pump with no mechanical moving parts that operates at pressures below about 1 mTorr. When pumping down from atmospheric pressure, a mechanical pump is used to reduce the pressure before the diffusion pump is switched on. High-speed fluid jets, generally of low volatility silicone oil, propel the pumped gas molecules, taking them to the bottom of the pump where they are expelled by a mechanical pump.
Diffusion pump. Courtesy of Edwards Vacuum Services
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digital-to-analogue converter (DAC) digital-to-analogue converter (DAC) A device, usually based on a semiconductor chip, which samples a digital signal, most frequently a voltage, and converts it into an analogue signal. The inverse operation is performed by an ADC.
digitisation Conversion of an analogue signal, generally a voltage, into a digitised signal. The DAC7714, courtesy of Texas Instruments
diode array detector (DAD) A detector that records the complete UV spectrum of an analyte as it elutes from an HPLC column. It can indicate the class of compound but the capacity factor, which is related to the retention time, is required for more accurate compound identification. The DAD is often used in series with a mass spectrometer to analyse the same solvent stream.
diradical An even-electron species with two free electrons, which act almost independently. Diradicals with both free electrons on the same atom include carbene and nitrene, :CH2 and :NH.
direct analysis in real time (DART)
Direct analysis in real time (DART). Analysis of artesunate tablets using DART. Courtesy of JEOL USA
A commercial ionisation technique that takes place outside of the mass spectrometer, at ambient temperature and pressure. A low velocity gas stream of metastable neutral atoms or molecules at ground potential is directed towards the sample on a surface. Ions produced from the sample are drawn into the mass spectrometer via a vacuum interface. Most surfaces and analytes are amenable and generally no sample preparation or preseparation is required. Analytes may be analysed in situ, such as illegal drugs on banknotes, fingerprints on glass and metabolites in plant tissue.
direct chemical ionisation see desorption chemical ionisation direct current (DC) An electrical current in which the electric charges flow continuously in the same direction, from high to low potential.
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direct exposure probe (DEP) direct exposure probe (DEP) A solid probe on which sample is deposited for insertion into the mass spectrometer source close to the electron beam (EI) or the reagent gas (CI). The probe is heated and the sample is volatilised.
direct insertion probe A probe for introducing samples, in which the sample is packed in a small holder, generally a quartz/glass capillary, and inserted into the mass spectrometer source close to the electron beam (EI) or the reagent gas (CI). The tube is heated to volatilise the sample.
Direct insertion probe. Courtesy of CDS Analytical, Inc.
direct liquid introduction (DLI) The direct introduction of a liquid flow containing analyte into the ion source, without any enrichment. The liquid is passed through a small orifice and naturally breaks up into droplets when the flow is optimised. The main drawback is the extreme vulnerability of the orifice to blocking. This method has been used for interfacing LC with EI and CI sources.
direct temperature-resolved mass spectrometry A form of pyrolysis MS in which the temperature of the sample is raised gradually to separate compounds in the evaporation phase from those in the crosslinked fraction of the pyrolysis phase. Commercial instrumentation tends to have a broader mass measurement range, up to m/z 1000, than pyrolysis mass spectrometers.
discrete dynode electron multiplier An electron multiplier comprising a series of dynodes for amplifying the ion signal from the mass spectrometer. The ions strike the first electrode, which produces secondary electrons that are accelerated towards the second dynode, which they strike and produce a greater number of electrons. This cascade effect continues down a series of dynodes to generate the amplified signal.
dispersion The spread of an ion beam as it traverses the analyser. Energy dispersion occurs when the ions have different kinetic energies, forcing them to
Discrete dynode electron multiplier. The IM-14642a-A Discrete Dynode Electron Multiplier, courtesy of SGE
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dissociative electron capture follow different trajectories. Angular dispersion occurs when ions having different trajectories as they enter the analyser are dispersed further. A mutual repulsion effect will also occur with ions of the same polarity. Dispersion has a direct effect on the resolving power.
dissociative electron capture A type of electron capture ionisation in which the resulting molecular radical anion dissociates rapidly via an intermediate state into an anion and a free radical. CF3Cl + e = CF3• + Cl-
dissociative ionisation The decomposition of a neutral molecule in the gas phase to produce at least one type of ion amongst the products. It applies to positive and negative ionisation.
distonic ion An odd-electron anion or cation in which the unpaired electron and the charge are located on different atoms. Strictly speaking, these are distonic radical ions. An example is +CH2-O-CH2•. The term also refers to multiply-charged ions in which the charges are separated onto different atoms.
dopant In APPI, the UV absorbing compound which is added to the solvent flowing into the source. It is excited by the source of photons in order to bring about secondary (chemical) ionisation of the analyte if the latter cannot be directly ionised by the light source.
double bond equivalent (DBE) see rings and double bond equivalents double focussing mass spectrometer
Double focussing mass spectrometer. Courtesy of the University of Bristol
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A mass spectrometer consisting of a magnetic sector and an electric sector in series which focusses ions that have differing initial momentum and kinetic energies. When the electric sector comes first, in the EB configuration, the arrangement is known as forward geometry.
doubly-charged ion Conversely, the BE configuration is known as reverse geometry. Two EB configurations are NierJohnson geometry and Mattauch Herzog geometry. In the former, a deflection of /2 rad in E is followed by a deflection of /3 rad in B to focus the ions at a focal point. In the latter, a deflection of /4√2 rad in E is followed by a deflection of Ⲑ2 rad in B to focus the ions on a focal plane. Also called a sector mass spectrometer
doubly-charged ion An atom or molecule that has an overall charge state of two. It can be produced by the loss of two electrons to create a doubly-charged cation, or by the gain of two electrons to create a doublycharged anion. It is also referred to as doublecharged ion.
dried droplet method A method for sample preparation for MALDI MS. A solution containing the matrix compound and the analytes is deposited on the sample stage and allowed to evaporate in a stream of air or nitrogen. The technique can be used for other variations of the laser desorption and ionisation technique. See also vacuum evaporation method, fast evaporation method, sandwich method.
droplets, electrospray see electrospray drying gas An inert gas introduced into the spray region of spray-based AP sources to assist evaporation of the solvent from the droplets formed. Nitrogen is used in most cases and the gas is generally heated.
duty cycle A pulsed ion analyser, such as a TOF, can only sample an ion beam for a fraction of time, defined by the period it takes for the detector to complete one complete analysis. The overall efficiency of detection is referred to as the duty cycle and expressed as a percentage of the total signal admitted to the analyser. Also used to express the limited time (dwell time) spent during a scanned spectrum on any single m/z value compared to that for a single ion SIM or MRM experiment.
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dwell time dwell time During SIM, the length of time allocated for measuring a particular ion or ions. It can be adjusted so that specified ions can be measured for longer periods, increasing the sensitivity of detection. The term is also used in MRM to describe the time taken to analyse a particular transition. In an ion trap CID experiment, the dwell time is adjusted to increase or decrease the collision time with the added gas.
dynamic exclusion
Dynamic exclusion. Representation of the process of dynamic exclusion in an ion trap using Pulsed Q-dissociation (PQD) Courtesy of Thermo Scientific
Resonance Excitation Amp
Step 1: Activation at High Q – PQD Time
Step 2: Delay at High Q – HQD Time
Main RF Amp
Kinetic Energy Internal Energy Fragment Intensity 0
100
200
300
400
500
600
700
800
900
Time (μsec) Step 3: Pulse to Low Q and Trap Fragments
Schematic of Pulsed Q Collision Induced Dissociation Process, a commercial implementation of a collision energy regime for a linear ion trap. Courtesy of Thermo Scientific
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The exclusion of particular ions from MS scans. It is used in CID to prevent an ion that has been selected for dissociation from being reselected for the next few scans over a defined time interval. It allows data to be collected on more components in complex samples. It is also used to exclude particular ions from analysis, such as those from background ions and known interfering compounds.
dynamic range 1. In a detector, a measure of the range of the number of ions that can be measured at one time. It is generally given as a power of ten obtained by dividing the maximum ion count by the minimum ion count. For a detector counting from 10 to 1 million ions, the dynamic range is 105. For mass spectrometers that generate large numbers of ions, such as TOF instruments, the detector can become saturated, limiting the dynamic range. 2. In quantitative analysis a measure of the range of concentrations over which successful quantitation can be achieved.
dynode A component within an electron multiplier that amplifies the number of secondary electrons. Electrons produced when the detected ions strike the first electrode are directed towards a dynode which they strike to produce a greater number of electrons. This cascade effect continues down a series of dynodes to generate the amplified signal. Discrete dynodes are also employed as the first element in a Daly detector.
2E scan
E 2E scan A sector instrument scan in which the electrostatic analyser voltage is set to transmit ions with twice the value required for the principal ion beam. Product ions of appropriate kinetic energy to charge ratios are detected from a collision cell in a field free region before the E and B sectors. Useful for analysis of partial charge transfer reactions such as: A++
+
Neutral
→
A+ +
[N]+
E Symbol for an electrostatic analyser.
E2/V linked scan This scan analyses the product ions formed in a field free region in front of the E and B sectors. The electrostatic analyser and accelerating voltage are both scanned in a manner which maintains a constant E2/V ratio.
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e/m e/m Ratio of electronic charge to mass.
Edman degradation Sequencing the residues in a peptide by stepwise removal of derivatised N-terminal amino acid residues by reaction with phenylisothiocyanate to release the amino acid as its phenylthiohydantoin derivative. The reactions are shown in the Figure. The usual analytical technique to determine which amino acids have been removed is HPLC, but MS can be employed to analyse both the residues and the contracting peptide chain. Edman degradation
Einzel lens A lens designed to focus an ion beam. It consists of three elements, two outer ring electrodes or cylinders at equal or ground potential and a central element at a higher or lower voltage.
elastic collision A collision between two particles in which the total kinetic energy is conserved. See also inelastic collision
elastic scattering see elastic collision electrochemical reaction A 3 cylinder Einzel lens. Courtesy of Dreebit GmbH, Germany
A chemical reaction obtained by virtue of electron removal or addition (oxidation/reduction) in a cell. It is especially relevant to the electrochemical cell which is created in an ESI source.
electrohydrodynamic ionisation A term from the 1970s for what was essentially ESI applied to solutions of inorganic salts such as sodium iodide in which cluster ions were produced. Relatively non-volatile solvents such as glycerol were employed and the ionisation occurred without the application of heat, making it suitable for thermally labile materials.
electron The elementary particle of (negative) charge. Symbol e.
electron affinity The energy (enthalpy) change associated with the 48
electron capture dissociation (ECD) attachment of an electron to an atom or molecule. In MS, it is an important parameter in defining the chances of success in forming a radical anion in an electron capture ion source.
electron capture dissociation (ECD) 1. A radical anion formed in an electron capture ion source frequently carries an excess of energy and will fragment by loss of a free radical leaving an even-electron anion. It is common practice to derivatise the analyte to create a species with a high affinity for an electron. It is important that the subsequent dissociation leaves the portion of the molecule representing the analyte as the charged anion. In the example shown in the figure a carboxylic acid RCOOH has been derivatised as the pentafluorobenzyl ester. The charge, after dissociation, is retained by the acid analyte. 2. In an FTICR MS instrument, a technique for ion dissociation using a beam of low-energy electrons. A valuable method for inducing the dissociation of multiply charged precursor protein ions which fragment to structurally informative product ions with minimal loss of PTM moieties. See also electron transfer dissociation
ECD of a pentafluorobenzyl ester derivative of an acid
electron capture ion source In both a NICI source and an APCI source, there is a significant population of low-energy ‘thermal’ electrons which can react with an appropriate analyte possessing high electron affinity to form radical anions. Typically, molecular radical anions of low internal energy are produced, allowing easy access to molecular weight information.
electronegativity A parameter which defines the relative electron affinity of the elements.
electron energy The potential difference through which electrons are accelerated in an EI ion source.
electron impact A frequently used term to describe the ionisation process taking place in EI. As no ‘impact’ really occurs, the term electron ionisation is preferred.
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electron ionisation (EI) electron ionisation (EI) The process of ionisation whereby an energetic electron passes sufficiently close to the outer shell of an atom to interact with and displace one of its electrons, leaving a radical cation: M + ε →
M+
●
+ 2ε
The efficiency of the process is often less than 0.1% but, because MS ion detection is efficient, the overall limits of detection are low.
electron ionisation desorption see desorption electron ionisation electron mass Electron multiplier (EM). Photograph by Tony Mallet
The mass of the electron, at 9.1094 x 10-31 kg. This parameter needs to be taken into account when calculating the accurate mass of ions for elemental composition determinations.
electron multiplier (EM) An ion detector in which the ions impact on a suitably prepared surface to emit a stream of electrons, which impact in turn on another surface, and so on, leading to successive amplification of the electron stream. It is finally detected and amplified by an appropriate circuit. Two forms of the EM exist, one with discrete emission surfaces (the discrete dynode EM) and another in the shape of a horn in which a continuous surface is present (the continuous-dynode EM or the channel EM).
electron transfer dissociation (ETD)
Electron transfer dissociation (ETD). Implementation of ETD in the Thermo Scientific LTQ Orbitrap XL - Courtesy of Thermo Scientific
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Reaction of a multiply charged protein or peptide ion with an anion in order to promote fragmentation by electron transfer. The anions are produced in a NICI source, generally from aromatic molecules with high electron affinities, and are introduced into the ion trap in which the protein/peptide ions are being held. Similar pathways of CID are observed to those observed in ECD with c and z fragment ions predominating, but the process can be implemented in a simple quadrupole ion trap rather than in the FTICR MS required for ECD.
electron volt (eV) electron volt (eV) A physical constant of energy corresponding to 23.1 kcal/mol or 1.602 x 10-19 Joule. Not an SI unit.
electropherogram A chromatogram showing the variation of detector signal against time as a capillary electrophoresis experiment proceeds.
electrophoresis The directed movement of a charged particle under the influence of an electrical field. Commonly used to separate mixtures of substances by making them move through a medium in which they are differentially retarded, for example by size in a gel or by differential attraction to a charged surface or environment.
electrosonic spray ionisation (ESSI) A variation of ESI in which a supersonic nebulising gas is used in conjunction with a conventional ESI source to bring about efficient pneumatic spraying of the charged liquid. It produces narrow charge state distributions compared with most other ESI variants. ESSI can ionise large and labile molecules, including noncovalently bound complexes while retaining their conformational integrity.
electrospray ionisation (ESI) A solution of the analyte is sprayed from a fine needle held at a high voltage. With the addition of heat and drying inert gas flows, the solvent evaporates and a series of fine charged droplets is formed. As these diminish in size, the coulombic forces between ions of similar charge on the surface exceed the surface tension of the liquid and spawn ever smaller droplets, leading eventually to a solvent-free ion. This process takes place at AP, making this source ideal for coupling to LC separations. The ions formed are introduced into the high vacuum of the mass spectrometer through one or more small apertures or through a length of capillary tubing, assisted by efficient vacuum pumping. Careful design of the source is required to ensure any cluster ions are broken up and as much of the solvent as possible is removed while
An arrangement for electrosonic spray ionisation. Figure 1 taken from R.G. Cooks, Anal. Chem.2004 76 (14) 4050-4058
Skimmers
Spray Needle/Capillary
Analyte/Solvent droplets (spray)
Transfer capillary To Mass Spectrometer
Analyte/Eluent flow (syringe pump or LC)
N2(g) flow Cone
ATMOSPHERIC PRESSURE Pumping
Electrospray ionisation (ESI). Reproduced from ‘Mass Spectrometry Ionisation Techniques and Applications for the Analysis of Organic Compounds’, P. J. Gates et al, in “Current Methods in Medicinal Chemistry and Biological Physics”, Carlton A. Taft and Carlos H. T. P. Silva, Research Signpost 2007, 81-3080141-8
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electrostatic energy analyser (ESA) still retaining an unfragmented molecular ion. See also Rayleigh stability limit
electrostatic energy analyser (ESA)
Electrostatic analyser. Reproduced from Mass Spectrometry: Principles and Applications, E.de Hoffmann and V. Stroobant, p 144, © John Wiley & Sons, Ltd
An analyser that focusses ions according to their kinetic energies. A spread of kinetic energies in the formation of ions in a mass spectrometer source leads to a lowering of the resolving power. In a double focussing magnetic analyser, ions are passed between a pair of curved plates carrying an electrical charge. These disperse ions according to their kinetic energy but do not separate them according to their m/z values. A magnetic sector will also disperse ions according to their kinetic energies and by placing these two devices together in an appropriate fashion, ions of different energies can be focussed to a single focal point. The magnetic sector will also separate ions of different m/z values.
elemental composition The fact that the values of the atomic masses of stable isotopes are non-integral can lead to estimations of elemental compositions for ions for which the m/z values have been calculated with sufficient precision. In practice, as the mass increases, the acceptable error required to ensure that a unique elemental composition can be assigned diminishes rapidly, even when valency restrictions, degree of unsaturation etc. are taken into account. The software implementing this procedure has recently been extended to take into account the experimental isotopic distributions which have been determined in the region of the ion being examined. Even so at m/z values above 500, accuracies significantly below 1 ppm may be necessary to avoid ambiguities.
eluate The liquid or gas stream issuing from a LC or GC column which contains the separated constituents.
eluent The gas or liquid used to elute substances from a chromatographic column.
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enantiomer enantiomer One of a pair of optical isomers that are mirror images of each other, differing only in the way the atoms are oriented in space.
end cap One of two conical metal plates which form the entrance and exit shapes of a Paul ion trap. They are attached to, but electrically insulated from, the central ring electrode.
endogenous Originating within a system, such as endogenous peptides or proteins in a biological matrix.
endothermic reaction A chemical reaction which absorbs energy, usually heat or light.
enhancement of ionisation efficiency The co-introduction of multiple components into an API source has been observed to increase the overall ionisation response. This may be due to changes in the efficiency with which ions can desorb from the spray droplets. In an APCI source, switching off the corona discharge sometimes leads to large improvements in ionisation, perhaps because it permits a thermospray mechanism to operate. See also matrix effects
enolate ion Enols (α-hydroxyalkenes) form the negatively charged enolate ion by loss of a proton from the hydroxyl group. This reaction can occur for stable enols or for those formed from ketones with αhydrogen atoms either side of the carbonyl group. The figure shows the formation of an enolate ion by the action of a base on a ketone.
Enolate ion derived from acetone
enthalpy A thermodynamic term which describes the total internal energy of a system. Electron or proton affinities are measured by the change in enthalpy, symbol ΔH.
entropy A measure of the energy in a system which is not available for work, symbol S. It is often envisaged as the degree of disorder in a system. 53
environmental analysis environmental analysis MS is increasingly used in analysing the environment for elements and molecules which are toxic, harmful or otherwise unwelcome, and is in routine use in studies of land remediation.
enzymatic digest The reaction mixture resulting from the digestion of a peptide, protein, or mixtures of peptides and/or proteins with an enzyme such as trypsin, chymotrypsin, pepsin, endoproteinase Glu-C, endoproteinase Lys-C and endoproteinase Asp-N. This is a key step in many proteomics analyses.
enzyme A protein which catalyses a defined reaction of a biological molecule.
epimer One of a pair of stereoisomers which each have more than one chiral centre but which differ only in the configuration about one of these centres. The figure shows two epimeric hexoses. Two epimers. The arrows show the altered stereochemical centres
epitope A molecule or part of a molecule which possesses a three-dimensional shape that can be recognised by an antibody or other biopolymeric molecule.
even-electron ion An ion having all its electrons paired.
even-electron rule This states that ions with fully paired electrons are unlikely to lose a radical species in fragmentation but will tend to form product ions by loss of a stable neutral molecule.
exact mass The calculated mass of an ion or molecule using the accurate elemental masses of the most abundant stable isotopes present. This is compared to the experimentally determined accurate mass in order to arrive at a probable elemental composition.
excitation chirp see chirp
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exogenous exogenous A substance found within a system that originates from outside of that system, such as a drug.
exoglycosidase An enzyme which can strip carbohydrate moieties from proteins.
exothermic reaction A chemical reaction which releases energy, usually in the form of heat, sound or light.
exponential scan Magnetic analyser fields are usually scanned by covering each decade of m/z value in equal time periods. This gives rise to an scan law which is exponential in time but leads to identical peak widths for the detected ions over the whole mass range.
external calibration Errors in the assignment of the m/z scale can be corrected by the determination of the spectrum of a compound of known composition and hence exact m/z values. This correction is then applied to the spectrum of the analyte under study. This is most common in the case of TOF and ICR analysers. See also internal calibration
external standard In quantitative analysis, the addition of a solution of the target analyte of known concentration to the matrix being analysed to provide correction for losses during extraction, purification and variations in instrumental response from a mass spectrometer. The instrumental response for a series of solutions of this standard is measured using an identical method for sample extraction and processing. The real sample is then run and the concentration of the analyte is deduced from the set of responses for the external standard samples. To be distinguished from an internal standard. See also stable isotope dilution assay
extracted ion chromatogram (XIC) see selected ion chromatogram. extractor plate see repeller 55
Faraday cup
F Faraday cup
fast particle beam
analyte/matrix spot
analyte ions
+ +
+
+
+ + +
+
+
matrix ions
+ +
+
+
+
+
+ +
+
To mass spectrometer
+
desorbed secondary ion beam
probe tip extraction grid
focussing lens
Fast atom bombardment (FAB). Reproduced from ‘Mass Spectrometry Ionisation Techniques and Applications for the Analysis of Organic Compounds’, P. J. Gates et al, in “Current Methods in Medicinal Chemistry and Biological Physics”, Carlton A. Taft and Carlos H. T. P. Silva, Research Signpost 2007, 81-3080141-8
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A type of detector in which ions leaving the analyser strike a metal plate attached to the collector electrode. Positive ions in the beam are neutralised by electrons from the metal and negative ions are neutralised by the transfer of electrons to the plate. The resulting current is amplified and measured and is directly proportional to the number of ions and their charge. The detector response time is slow, limiting the spectrum scan speed, and it is less sensitive than an electron multiplier but provides a noise free and stable signal. For this latter reason it is favoured for use in stable isotope recording instruments. Also known as a Faraday cylinder and a collector.
Faraday cylinder see Faraday cup fast atom bombardment (FAB) An ionisation technique for non-volatile analytes employing a beam of neutral atoms, and occasionally molecules, which is directed towards the analyte deposited on a target plate. The analyte
fast evaporation method is dissolved in a matrix solution to ensure energy transfer to the analyte for desorption and ionisation. Typical matrices are glycerol, 3nitrobenzyl alcohol and a dithiothreitoldithioerythritol mixture. Inert gases such as argon or xenon are generally used as target gases at energies of several keV. In conventional FAB, the sample-matrix solution is applied to a probe and inserted into the mass spectrometer source. See also continuous-flow fast atom bombardment.
fast evaporation method A technique for creating a sample for MALDI analysis. A drop of the matrix solution is applied to the MALDI stage and allowed to dry as a thin film. A drop of the analyte solution is then applied over the film and also allowed to dry.
fast ion bombardment Similar to FAB but a beam of ions is used in place of the atomic beam. The most common sources use caesium ions (Cs+) at typical energies of 30 keV. Increased secondary ion yields can be obtained using molecular ions, such as Cs3I2+ or ionic clusters of gold, rather than atomic ions. Also known as LSIMS. The acronym FAB is used for both atom and ion bombardment.
femto The prefix for a factor of 10-15. Symbol f. As in 5 femtograms, or 5 fg.
field desorption (FD) An ionisation technique in which a very strong electric field, typically 107-108 V/cm, is produced between two electrodes, one of which is a metal filament coated with the analyte. The filament or emitter, typically made of rhenium or tungsten, is coated with carbon whiskers to increase the surface area and charge field density. The sample is applied as a solution which is dried to leave a solid deposit. The technique produces largely singly-charged protonated or deprotonated molecules and is suitable for non-volatile, thermally labile compounds. Also referred to as field desorption/ionisation.
Field desorption (FD). The tip of a FI/FD/LIFDI probe. Courtesy of Linden CMS GmbH, Germany.
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field desorption/ionisation field desorption/ionisation An older term used to describe FD. Since ionisation occurs in the condensed phase on or near the emitter, it could be argued that this is a more correct term than FD.
field-free region (FFR) A region in the mass spectrometer where there are no magnetic or electric fields to deflect ions.
field ionisation (FI) An ionisation technique closely related to field desorption but in which the sample is in the vapour phase and is allowed to pass over the emitters. These are the same as used in field desorption.
Field’s rule In fragmentations of different even-electron cations which form the same even-electron ion, the neutral fragment is more likely to leave without the charge for molecules having lower proton affinity. In the example here, where X can be O or S, formation of C2H5+ is favoured in the former case because O=CH2 has a lower proton affinity than S=CH2. C2H5-X=CH2+ → C2H5+ + X=CH2
filament A thin heated metal wire or ribbon element used to emit electrons or photons.
filtered noise field (FNF) A technique allied to broadband excitation which, when applied to a Paul ion trap, suppresses the population of matrix (background) ions permitting a larger population of a minor analytical component to be analysed without encountering the problems of space charging. Typical use would be for analysis of air samples for traces of volatile explosives.
fingerprint mass spectrum The characteristic mass spectrum of a compound from which it might be identified. It can be produced by various techniques, such as EI or pyrolysis MS or product ion MS/MS. For peptide fingerprinting, see mass mapping. 58
first stability region
first stability region see Mathieu stability diagram fishhook arrow The symbol used to indicate the movement of a single electron in reaction mechanisms.
fission fragment ionisation see californium 252Cf desorption flight tube The evacuated tube in a mass spectrometer through which the ions travel after acceleration.
floating In tandem MS with a collision cell, the potential applied to the collision cell is kept at a fixed value above earth (floated) to distinguish ions formed by CID from those arising from metastable decomposition. When the cell is floated, the kinetic energies of the metastable ions become differentiated from those of the product ions.
flowing afterglow A flow of an inert gas, typically helium, is passed through a microwave discharge and ions are formed from the trace amounts of water vapour present to produce a flowing afterglow. The ions are carried along a flow tube towards a reaction region, where analyte ions are introduced. Product ions from the resulting ion/molecule reactions are carried by the gas flow to the analyser. The main disadvantage is that all of the source-produced ions, secondary ions and others reach the reaction region, complicating the kinetic analysis. Trace amounts of other gas can be added to the initial flow to produce other reagent ions.
Flowing afterglow. Courtesy of Patrik Spanel and David Smith, Keele University, UK
flow injection The injection of a sample into a flowing liquid stream for mass spectrometric analysis without the use of a column.
flow injection/reaction analysis (FIA) The injection of an analyte into a flowing liquid stream that is fed to the mass spectrometer. In some cases, the liquid stream contains reagent ions, so that reaction occurs in the flowing liquid before entering the mass spectrometer.
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focal plane detector focal plane detector A detector in which spatially dispersed ions strike the detector plane at the same time, such as a photographic plate.
focussing 1. The focussing of ions of differing trajectories or kinetic energies in magnetic and electric sector instruments, either on their own or in combination in double-focussing instruments. Adjustment of the geometry of either sector allows correct focussing to occur. 2. Ion focussing is essential for good transmission through the parts of any mass spectrometer. This includes energy and momentum focussing and the use of RF-only multi-rod assemblies placed in tandem mass spectrometers.
forward geometry The set up of a double-focussing mass spectrometer where the electric sector precedes the magnetic sector. Symbol EB.
forward library search A method for library searching in which a spectrum is compared with each library spectrum in turn to find similar matches.
Fourier transform (FT) The mathematical operation used to convert the inductance current signal detected in an ICR trap or Orbitrap mass spectrometer to a set of m/z values. The Fourier components correspond to ion mass and the Fourier coefficients correspond to ion abundance. 14.5 T Actively Shielded Solenoidal Magnet g 104 mm Bore
Fourier transform ion cyclotron resonance mass spectrometer (FTICR) LTQ
Turbopump
Fourier transform ion cyclotron resonance mass spectrometer (FTICR). Courtesy of Alan Marshall, Florida State University, USA
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An ion storage device in which ions are trapped by crossed magnetic and electric fields and follow circular trajectories perpendicular to the magnetic field. They are excited to wider orbits by a radiofrequency pulse and the decay of their image currents is detected as time domain signals, later converted to m/z values by FT. Ion detection does not result in loss of the ions, so they can be stored for long periods in the ICR cell. This device is also referred to as a Penning trap.
fragmentation pattern fragmentation pattern The characteristic distribution of fragment ions in the mass spectrum of a particular compound, from which the compound might be identified. See also fingerprint mass spectrum
fragmentation reaction The reaction of a molecular or fragment ion with excess energy to produce a further fragment ion. It can occur by rearrangement or by decomposition.
fragment ion A product ion formed by fragmentation of a precursor ion. It may be stable or undergo further fragmentation.
fragment ion linked scan see linked scan fragmentor voltage A commercial term used by one manufacturer to describe in-source CID.
free induction decay (FID) In FTICR MS, ion packets in a Penning trap are cycled in phase between two detection plates to produce a signal known as a FID, transient, or time-domain data. This signal comprises a set of frequency signals from which the mass spectrum is extracted by performing a fast FT.
free path see mean free path free radical An entity with a single unpaired electron, . . designated by the dot symbol, as in Cl or CH3 .
Free induction decay (FID)
frequency domain In FTICR MS, the time-domain ICR signal is transformed into the mass-domain signal (the mass spectrum) via the frequency-domain signal.
FTMS see Fourier transform ion cyclotron resonance mass spectrometer
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full width at half-maximum height (FWHM) full width at half-maximum height (FWHM) The width (Δm) of a singly charged mass spectral peak (M) at a position corresponding to half of the peak height. It is used to determine the resolving power of a mass spectrometer by the ratio m1/Δm as in the Figure.
functional group Full width at half-maximum height (FWHM)
An atom or collection of atoms with characteristic chemical properties that is part of an organic compound, such as nitro, hydroxy or carboxylic acid groups.
functionalised molecule A molecule which has been modified to introduce a functional group in order to change the chemical and/or physical properties. In MS, this may be carried out to render a compound volatile for GC/MS, to generate a more informative mass spectrum, or to create specific fragmentation pathways.
functional proteomics The study of the functions of expressed proteins in biological systems and how they interact with each other and with other biomolecules.
FWHM see full width at half-maximum height
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gain
G gain Electrical signals, measured in volts, can be amplified by appropriate circuitry. The degree of amplification is often called the gain. Thus, an electron multiplier detector can be said to have a gain of 106, indicating that it will amplify the incoming signal one million times.
Ensures the optimum number of ions are in the trap at all times Automatically adjusts the ionization time as ion flux into the trap changes Prevents space charging
gamma hydrogen A hydrogen atom attached to the atom four carbon atoms distant from the original charge site. In the Figure, the gamma hydrogen atom is transferred to the six-membered ring.
Representation of automatic gain control – Courtesy of Thermo Scientific
gas ballast The oil in rotary vacuum pumps will absorb solvents, water and gases removed from mass spectrometers. In order to maintain efficiency and prevent corrosion of the pump components, a period of pumping with the admission of a bleed of air - called gas ballasting - is regularly recommended.
Rearrangementof a ␥-hydrogen atom
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gas chromatography (GC) gas chromatography (GC) Separation of mixtures of compounds in their gaseous state can be achieved by passing them in a stream of heated inert gas, called the carrier gas (usually helium or hydrogen) through a long column containing an immobilised stationary phase for which different components will have different affinities. The column is held in an oven at a carefully controlled temperature. The stationary phase can be chemically bonded to the internal wall of a silica capillary column or can be adsorbed onto a porous inert medium which is packed into a glass spiral column. The sample, either in gaseous form or dissolved in a low boiling solvent, is injected on to the top of the column into a heated chamber and the gaseous mixture is passed through the column. It is common to use a temperature gradient to heat the column. Separated components elute from the end of the column and are passed to a detector.
gas chromatography-combustion-isotope ratio mass spectrometry (GCC-IRMS) Precise and accurate isotope ratio determinations of organic molecules from biological sources can be obtained by passing separated compounds from a GC column through a combustion device in which carbon is converted to carbon dioxide. The 12 C/13C ratio of the product is determined on-line in a SIRA mass spectrometer.
gas chromatography/mass spectrometry (GC/MS)
Exact Mass GC/MS: Waters ® GCT PremierTM orthogonal acceleration time-of-flight mass spectrometer. Image courtesy of Waters Corporation. www.waters.com/gcms
Direct coupling of the output from a GC to the source of a mass spectrometer is a relatively simple exercise. If helium is used as the carrier gas with a capillary column, a modern EI mass spectrometer source can easily be pumped to remove up to 1 ml/min gas flows. Higher flow rates from packed columns require some flow splitting prior to the source. EI and CI are the most common forms of ionisation in use with GC but coupling to an ESI atmospheric pressure source has been reported.
gas molar constant The pressure (P), volume (V) and temperature (T) of an (ideal) gas are related to the molar quantity 64
gas-phase acidity and basicity (n) of that gas by the equation: PV=nRT where R is the gas constant.
gas-phase acidity and basicity These terms refer to the free energy change associated with the addition of a proton to the molecule in the gas phase. In AP ion sources, ions are frequently formed by this chemistry and the success or failure in obtaining an ion from an ESI or APCI ion source will depend on the thermodynamics of these processes.
gas-phase fractionation When CID spectra are recorded from a chromatographic inlet, only the most intense precursor ions are selected. Other, less abundant ions are ignored, some of which may be important. An alternative procedure is to divide (fractionate) the mass spectrum into several smaller, overlapping m/z ranges and select several precursor ions from each of these ranges, so expanding the coverage. It is most commonly used in the analysis of peptide mixtures produced by the digestion of protein mixtures, leading to the identification of more peptides and, ultimately, more proteins.
gate, ion see ion gate Gaussian peak A symmetrical peak describing a normal distribution. This is shown in the figure and is the ideal shape for an ion signal from a magnetic analyser and is also the shape the data system will produce for ion signals from quadrupole analysers. TOF and ICR analysers tend to have Lorentzian peak shapes.
Gaussian peak
gel permeation chromatography (GPC) A form of LC in which the stationary phase is composed of a gel with pores of defined sizes. Mixtures of compounds separate according to the extent that they are retained in the pores and elute in order of molecular size with the largest species eluting earliest. Also known as size exclusion chromatography. 65
genetic engineering genetic engineering The science of manipulation of the genome to seek improved expression of the function, for instance in improved disease resistance in a plant species.
genomics The study of the science of genes. In MS, analysis of the constituent nucleotides is an area of importance but the most frequent use of the technique is in the analysis of the proteins in the proteome.
glow discharge mass spectrometry (GDMS)
Glow discharge mass spectrometry (GDMS). Schematic diagram of direct current (dc) glow discharge mass spectrometer (VG 9000). (Reproduced by permission of GV Instruments Ltd)
Elemental analysis in which a solid sample, often in the form of a rod, is directly ionised in an argon plasma. The glow discharge describes the formation of a plasma in a cell in which the sample is placed as the cathode with the cell itself as the anode. Argon at approximately 1 Torr pressure is typically subjected to a voltage of 1 kV to produce positively charged argon ions which impact on the sample, leading to the release of neutral elemental atoms which become ionised in the plasma by interaction with metastable argon ions. The sample ions are then analysed in a mass spectrometer.
glycerol A common matrix compound employed for FAB ion sources. It has the advantage of being relatively involatile and long lasting in high vacuum and of producing only a few clearly characterised cluster ions in FAB MS.
glycomics Studies involving the sugar residues attached to large biologically active molecules such as glycoproteins.
glycoprotein
A glycoprotein showing the peptide chain and a branched carbohydrate chain
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Many proteins are post-translationally modified by the addition of large linear and branched chains of carbohydrate molecules. They attach to the nitrogen in asparagine or to oxygen in serine or threonine.
gradient elution gradient elution The controlled formation of solvent mixtures in HPLC experiments where the solvent composition is changed from a starting defined percentage of one solvent to a different composition over a stated time interval. While it is common to use two solvent systems, three or four can be employed. For two solvents this can be achieved either by the use of two high pressure solvent pumps or by a proportioning mixer device placed before a single pump.
grid An array of fine wires used to deflect and focus a beam of ions.
gridless acceleration TOF mass spectrometers, in early designs, used grids to apply accelerating and focussing voltages to the ion beam and in the reflectrons. As an alternative, beam focussing can be achieved by the use of lenses. Although more complex designs are required, greater resolving power is an important result.
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Hadamard transform
H Hadamard transform A generalised type of Fourier transform, which uses square waves rather than sinusoidal waves for signal conversion. This transform has been employed to deconvolute overlapping TOF signals such as those that occur when the rate of the ionisation pulses exceeds that at which the data is being collected. This technique is designed to improve the duty cycle of such instruments.
Hall probe
A temperature controlled Hall probe designed to fit between the poles of a magnet in a double focussing mass spectrometer. Photograph by Tony Mallet
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A detector, often a thin plate of a conductor or semiconductor, that measures magnetic flux density, used in magnetic sector mass spectrometers to control scanning. It relates the m/z value of an ion to the magnetic field strength needed to deflect it onto the detector, following calibration with a calibration compound. The controlling data system uses signals from the probe to program the DAC to produce the required voltages needed to change the magnetic field strength during scanning and to minimise the effects of hysteresis.
hard ionisation hard ionisation Ionisation which produces significant fragmentation of the target compounds, such as that achieved by EI.
heated pneumatic nebulizer Ion sources using API need to produce fine droplets with as little solvent as possible. The application of heated nitrogen as a nebulising gas serves to assist this process.
hecto The prefix for a factor of 102. Symbol h. As in 5 hectograms, or 5 hg.
helium The inert gas, symbol He, used as a collision gas in high-energy collision cells for tandem mass spectrometric experiments. It is also used as a buffer/collision gas in ion traps and as a carrier gas in GC/MS experiments.
heterolytic fragmentation A type of ion fragmentation in which a bond is broken by the transfer of a pair of electrons from the bond to the charged atom. In alpha cleavage, a bond alpha to the charged atom is broken and in beta cleavage, a bond two removed from the charged atom is broken. The movement of 2 electrons is signified by a double-barbed arrow. Also referred to as charge-induced fragmentation. The fragmentation of an even-electron ion is shown in the figure. Heterolytic bond fragmentation
hexapole A device containing six rods used as an ion guide to focus divergent beams of ions, as a storage device to accumulate ions before transfer to another part of the system, or as a collision cell. RF voltages are generally applied to the rods. See also octapole
A hexapole ion focussing lens. Photograph by Tony Mallet
high-energy collision In CID of ions with an inert gas, the employment of ion energies of 1 keV or greater, usually with a single collision. The collision gas in these experiments is typically helium, argon or xenon.
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high-field asymmetric waveform ion mobility spectrometry high-field asymmetric waveform ion mobility spectrometry (FAIMS)
High-field asymmetric waveform ion mobility spectrometry (FAIMS). Ions oscillating between the FAIMS plates. Courtesy of Roger Guevremont, www.faims.com
A form of IMS in which ions are separated using a periodic asymmetric electrical waveform applied to two electrodes, which generates alternate high and low electric fields. As ions are transported along a flow tube by a carrier gas and a low DC voltage, the waveform causes them to oscillate and they drift towards either of the electrodes and collide with the residual gas present. The variable low DC voltage (the compensation voltage) compensates for the drift, resulting in ion transport into the mass spectrometer. Separation is based on differences in the overall three-dimensional shape of the molecule and in the distribution of charge on the ion. FAIMS can operate at atmospheric pressure or higher, up to 1500 Torr. See also ion mobility spectrometry
high performance liquid chromatography (HPLC)
High performance liquid chromatography (HPLC). HPLC and HPLC/MS: Waters® Alliance® HPLC System and the 3100 single quadrupole mass detector. Image courtesy of Waters Corporation. www.waters.com/ms
A type of column chromatography which separates analytes in liquid mixtures so that they can be analysed separately. The liquid is added to a column containing a packed stationary phase through which a moving phase of solvent is passed. The differential effects of retention by the stationary phase and elution by the moving solvent phase separate the substances as they pass down the column. HPLC evolved from LC in the 1970s when smaller stationary phase particles were found to give better separations but required positive pressure to force the solvents through. This led to the name high pressure liquid chromatography, which has gradually been replaced by high performance liquid chromatography. HPLC is often referred to as LC.
high-pressure mass spectrometry MS in which the source operates around atmospheric pressure. The technique is used to study the properties, energetics and reactions of ions and clusters.
high resolving power A resolving power of 10,000 or greater. This value is sufficient to separate two peaks at m/z 100.00 and 100.01 with a defined valley. Values this high 70
high-throughput screening are achieved in FTICR and TOF mass spectrometers, linear ion trap-Orbitrap hybrid instruments and in sector instruments but not in quadrupole analysers.
high-throughput screening The large-scale study of libraries of lowmolecular-weight compounds for biological activity, especially in drug discovery. Typically, thousands of compounds synthesised by combinatorial chemistry techniques, or collections of natural compounds, are tested for activity against target molecules, enzymes or cellular systems. Active compounds (hits) are investigated further. It is also used for testing the stability of large groups of compounds.
high vacuum Certain regions of the mass spectrometer are pumped down to pressures of O, S >> N, C. Similar conditions apply to an odd-electron ion.
inductively coupled plasma mass spectrometry (ICPMS)
Gate valve Ion detector Quadrupole Sampler ICP torch Nebulizer/Spray chamber
(c) Quadrupole dynamic reaction cell in Elan DRC
Detector Mass Analyzer
Ions to Detector Mass Analysis of Transmitted Ions
(b) Elan DRC
Reaction Cell
Interface Cones Lens
Isobar Analyte Other m/z Conversion of Ions from Source Reactive Ions
Pumping system
(a) Elan 9000
Inductively coupled plasma mass spectrometry (ICPMS). Schematic of ICP-QMS Elan 9000 without collision cell. Reproduced by permission of Perkin Elmer, Germany
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A technique for elemental analysis in which an argon plasma is used to ionise the sample from a sprayed solution. Free charged atomic cations are produced in the intense heat of the plasma and these are analysed online with a mass spectrometer, by introduction through a specialised AP source. Individual isotopic forms are distinguished and quantified.
inelastic collision A collision between two particles in which the total kinetic energy is not conserved but a part is
information-dependent acquisition (IDA) converted into internal energy. This can lead to ion fragmentation in a CID experiment.
information-dependent acquisition (IDA) The acquisition of data after particular conditions have been met in a mass spectrum. For example, data-dependent MS/MS spectra are recorded in real time for the n most intense ions in a mass spectrum, where n is defined by the analyst.
infrared multiphoton dissociation (IRMPD) Ion dissociation by absorption of several photons from an infrared laser. This technique provides an additional means of fragmenting ions for tandem mass spectrometry experiments. IRMPD is resonance excitation-led while SORI CAD is charge mediated, and the two methods can operate through different pathways of fragmentation.
in-source CID In MALDI, ESI and APCI sources, ion fragmentation can take place either in the ion source or after the ions have exited from it. The former case is referred to as in-source CID and the fragment ions, which will have identical velocities to the precursor ion, can be separated and analysed by a reflectron. Also known as prompt fragmentation.
instrumental limit of detection A measure of instrument performance based on the instrumental signal-to-noise ratio or the variability of a standard blank sample. Unlike the limit of detection, it does not depend on the sample matrix, since it is measured in the absence of sample.
integral molecular mass The RMM calculated using integral values of the elemental isotopes present in the molecule. See also relative molecular mass, accurate molecular mass.
intensity Ion intensity is used to describe the signal measured for the detected ion in a mass spectrometer. The preferred term for a set of ions in a spectrum is ion abundance as this reflects the distribution of the different isotopic species. 75
interface interface A general term to describe the means of linking one instrument with another, as found in a GC/MS system. A typical interface here would be the heated line down which a capillary GC column is fed directly into an EI source.
internal calibration In order to improve and confirm the calibration of the m/z scale of an analyser, the inclusion of a compound forming an ion or ions of known formula and therefore known exact mass, together with the analyte. This permits the further revision and recalibration of the m/z scale for a spectrum containing that ion. It is a common procedure to improve the accuracy of m/z measurement in MALDI-TOF mass spectra. See also external calibration
internal energy The energy residing in the ion after ionisation or after CID which may result in fragmentation. Whether or not a fragment ion is detected depends on both the thermodynamics and the kinetics of the processes involved.
internal fragment
Internal fragment after a double cleavage on CID of a peptide chain
Fragmentation of peptide ions by CID can lead to product ions formed by cleavage of two or more internal bonds of the peptide chain losing parts from both the C and N terminals. Most frequently, these involve a combination of b and y type fragments. While mostly formed of two or three amino acid residues, internal fragments are of low abundance in product-ion spectra except where a proline residue is involved. The structure of the product ion is shown in the figure. See also immonium ion
internal standard A compound added in a known quantity to the matrix to be analysed in quantitative analysis that is extracted and purified together with the target analyte. It is separately detected and analysed in the mass spectrometer. The ratio of the ion abundance of the analyte to the internal standard signal is measured and converted into a concentration unit via an appropriate calibration 76
intramolecular fragmentation curve. The differential detection by the mass spectrometer can be achieved either by a difference in m/z of the detected ion or by a different elution time from a chromatographic inlet system, or both. See also external standard, volumetric internal standard, stable isotope dilution assay
intramolecular fragmentation Fragmentation of an ion formed by EI is a unimolecular process. When rearrangement reactions are involved these are necessarily intramolecular.
inverted magnetron gauge A cold cathode ion gauge in which a stream of electrons produced by a high voltage ionises residual gas molecules. These are allowed to impinge on a cathode under the influence of electric and magnetic fields. The current which flows is a function of the pressure. This type of gauge can be used from 10-2 to 10-10 mbar.
ion An atom, molecule, any fragment of a molecule or any other particle which carries a positive or negative electrical charge.
ion counting detector The time-to digital converter used in TOF MS is an ion counting detector. Electron multipliers can be operated in ion counting mode. The common output is a digital stream of data as opposed to an analogue one.
Inverted magnetron gauge. Courtesy of INFICON Limited, Liechtenstein
ion cyclotron resonance (ICR) An ion constrained in a magnetic field in a threedimensional Penning trap will move in a circular orbit. This cyclotron motion has a frequency ωc which depends, among other parameters, on the m/z value of the ion. The equation of motion can be written as ωc = zB/m where B is the magnetic field strength. The m/z of the ion can therefore be determined directly from 77
ion dissociation the value of the cyclotron frequency. A mass spectrometer based on this principle is an ICR MS. See FTICR MS
ion dissociation The fragmentation of one ion into a second ion of lower charge and other ions or neutral species. A singly-charged ion can dissociate into a lower mass ion plus a neutral species. Multiply-charged ions can dissociate into two or more ions of lower charge.
ion energy loss spectrum A spectrum that plots the loss of translational energy of ions involved in ion/neutral reactions against their relative abundances.
ion evaporation model One theoretical treatment of the formation of ions in an ESI source (see also charge residue model) in which ions are ejected directly from the charged droplet.
ion exchange chromatography A type of chromatography in which the stationary phase is an anion exchange or cation exchange resin for trapping ions of the opposite charge from the sample solution.
ion funnel In order to improve the ion transmission efficiency of AP ion sources and the products of CID, a number of focussing devices have been designed to focus the ions, after initial formation, into a narrow collimated beam that can most efficiently be introduced into the analyser. The ion funnel is a recent implementation of this, comprising a set of many ring electrodes fed with a combination of RF and DC voltages which serve to produce the focussing effect.
ion gate
Ion funnel. Photograph by Tony Mallet
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In a TOF MS instrument, this is an arrangement of ion focussing elements to deflect ions of a defined m/z range. Often used to suppress the many low m/z ions formed from ionisation of the matrix in a MALDI source.
ion guide ion guide A device for transferring ions from one segment of a mass spectrometer to another. Designs include multipole and electrostatic focussing devices.
ion imaging see imaging mass spectrometry ionisation The formation of an entity carrying an electrical charge.
ionisation cross section The probability of ionisation of a molecule following reaction with an electron or photon or another ion or molecule.
ionisation energy The minimum energy required to produce a molecular ion, M+ from its ground neutral state M. ●
ionisation gauge A device which records the pressure in various parts of the instrument. See Pirani gauge, Penning gauge, inverted magnetron gauge, thermal gauge, McLeod gauge
ionisation plasma The argon plasma in ICPMS and the corona discharge in the ion source in APCI.
ionisation potential see ionisation energy ionisation suppression A matrix effect occurring in ion sources in which ionisation of an analyte is suppressed by the presence of a coeluting matrix component.
ionisation threshold The minimum energy of the laser beam which will produce ions from the analyte in a MALDI experiment. This is often the value at which optimum mass resolution is obtained.
ion kinetic energy spectrometry (IKES) This technique for the analysis of CID or metastable reactions uses an electrostatic analyser 79
ion lens (E) or a BE double focussing mass spectrometer. The parent ion has to be selected manually and product ions can be detected by scanning the electrostatic analyser. The advent of reversed geometry mass analysers in which the parent ion can be selected in the magnetic sector, led to this technique being superseded by MIKES. See massanalysed ion kinetic energy spectrometry
ion lens A device to change the direction of motion of the ions, used principally for the focussing and defocussing of ions.
ion microprobe A primary high-energy ion beam for SIMS which is designed to act on a small area of the target sample. Typical beam dimensions are in the tens of nanometres.
ion mirror see reflectron ion mobility spectrometry (IMS)
Ion mobility spectrometry (IMS). LC/IMSMS: Waters® SYNAPT™ G2 HDMS™ quadrupole time-of-flight/ion mobility MS system. Image courtesy of Waters Corporation. www.waters.com/msms
The passage of a mixture of ionised molecules through a region of relatively high pressure inert gas leads to a difference in transit times based upon their different behaviour on collision with the background gas. This distinction reflects differences in the three-dimensional structures of the molecules. It is now common to combine IMS with a mass spectrometer to detect and characterise closely related ions of identical m/z but of differing three-dimensional shapes. The combined technique is often used to distinguish biological molecules of distinct three-dimensional shapes. See also FAIMS
ion/molecule reaction The chemistry of reactions between ions and neutral molecules can be examined by MS in ion traps and collision chambers. The reaction between an ion and a molecule is among the fastest of all chemical reactions. Activation energy barriers are nearly zero and the rate depends only on the chances of a collision occurring. A common example is the use of CI with a reagent gas.
ion-neutral complex The transition state species which arises between a precursor ion and its reaction products. 80
ion/neutral reaction ion/neutral reaction The reaction of an ion with an atom or molecule.
ion optics The totality of ion focussing devices in a mass spectrometer. These are present in the source, interface from source to analyser, analyser(s), collision chambers and detector.
ion pair formation The formation of both positive and negative ions from a fragmented molecule as shown in the figure.
Ion pair formation
ion reflector see reflectron ion source The part of the mass spectrometer used for sample ionisation, since only particles which carry an electric charge can be analysed in a mass spectrometer. A variety of ion sources are in common use, each designed to ionise a specific class of atom or molecule. See also electron ionisation, chemical ionisation, electrospray ionisation, etc.
ion spray A commercial term for one manifestation of electrospray, which in practice is pneumatically assisted electrospray. Most modern electrospray sources are pneumatically assisted. Also known as IonSpray or ionspray.
ionspray see ion spray ion trap A three-dimensional space defined by metal surfaces carrying DC and RF voltages in which ions can be held for extended periods of time. In ICR traps (Penning traps) a powerful magnetic field is also present. See also Paul trap, Penning trap, linear ion trap, Orbitrap
isobaric interferences In ICPMS, the signal for a specific isotope of an element is often obscured by overlapping signals due to background gases or compounds producing isobaric ions of nearly identical m/z. A common
Ion Trap
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isobaric ions problem arises with argon oxide and iron with m/z values of 55.9573 and 55.9354, respectively.
isobaric ions Ions differing in composition but having identical m/z values. Thus, at a nominal m/z of 180, C8H12N4O and C10H14NO2 differ in mass by only 1.3 millimass units.
isobutane A gas, (CH3)3CH, in common use in CI where it provides low-energy ionisation by transfer of a proton to the analyte.
isomers Molecules which vary in their three-dimensional structures. These include structural, geometrical and optical isomers. MS can distinguish between certain types of isomers but is not always the method of choice.
isotope While the nature of an atom is defined by its number of protons (and electrons), the number of neutrons can vary over a small range. These different species are called isotopes. Not all isotopes are stable, many are radioactive. MS was the technique originally used to discover them (Aston, 1920).
isotope-coded affinity tag (ICAT)
The process of stable isotope protein tagging to establish protein expression. Courtesy of Dr Kate Heesom, University of Bristol, UK
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In order to establish the relevance of a protein to an organism’s phenotype, it is important to be able to determine quantitative changes in its expression. This can be achieved by labelling with a compound (tag) which contains stable isotopes such as 2H. One batch of the organism is tagged with the heavy form of the label, containing the stable isotopes (2H), and another batch is tagged with the light form, containing 1H. The reactions are specific for cysteine residues within the proteins. The labelled samples are mixed and digested with trypsin and the isolated peptides are analysed by LC/MS/MS, enabling the relative abundances of each peptide pair, containing the light and heavy label, to be determined. ICAT is a commercial term.
isotope dilution isotope dilution see stable isotope dilution assay isotope fractionation Small changes that occur in the naturally occurring abundance ratios of isotopes of the elements present during the chemical reaction of a molecule. They arise because the bond energies of each isotope are slightly different. Similar changes will occur when gaseous samples are allowed to diffuse or are passed through valves and tubes.
isotope labelling The substitution of one or more atoms in a molecule with a less abundant stable elemental isotope, commonly deuterium (2H), 13C, 15N or 18 O.
isotope ratio mass spectrometry (IRMS or SIRA) In the course of metabolic reactions or geologic time and radioactive decay, the naturally occurring ratios of isotopes present will change. Measurement of the ratios provides information about these processes and about the age of specimens containing these elements. Specialised mass spectrometers can deal with gaseous samples and samples introduced through a chromatographic system. EI is the most common ionisation technique although AP techniques are being developed. Often very small ratios are involved and even smaller changes have to be detected with high precision.
isotopic abundance see natural isotopic abundance isotopic purity In surrogate internal standards, the degree to which stable isotopic substitution has been achieved in a synthetic product.
isotopologue ions Ions which differ in their isotopic composition but retain the same elements, e.g. H2O and HDO.
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isotopomer ions isotopomer ions Ions which are identical in their isotopic composition but in which the positions of the isotope substitutions differ. It is a contracted form of the term isotopic isomer. CH2DOH and CH3OD are examples.
iTRAQ A commercial term for a technique similar to that using ICAT reagents for measuring relative changes in the expression level of proteins. Each protein sample is digested with trypsin and the peptides formed are labelled with the iTRAQ reagents at the N-termini. Up to four reagents are employed, differing only in the degree of isotopic substitution. The labelled peptides from the two samples are combined and subjected to LC/MS/MS analysis enabling the relative abundances of each peptide pair to be determined.
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JCAMP-DX
J JCAMP-DX A universal ASCII format for spectroscopic data. It was devised to simplify digital data transfer between computerised data systems at a time when the data formats from various instrument manufacturers were proprietary. It was defined by a IUPAC Joint Committee on Atomic and Molecular Physical Data originally for IR data and has now been extended to other spectroscopic techniques, including MS.
jet desorption ionisation (JeDI) A variation of DESI in which a high-velocity jet of an aqueous solvent under high voltage (2-6 kV) is directed towards the sample at ambient pressure and temperature. Impact of the jet produces small, charged droplets which contain species originating from the surface that are drawn into a mass spectrometer for analysis. Unlike DESI, JeDI can penetrate the surface to produce three-dimensional imaging and has been used successfully with heart tissue in vivo.
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jet separator jet separator
Jet separator. Reproduced with permission from Practical Organic Mass Spectrometry – 2nd Edn, J.R. Chapman, John Wiley & Sons, Ltd, © 1993
A type of GC/MS interface which removes most of the carrier gas molecules from the GC effluent before entering the mass spectrometer, thereby maintaining the vacuum. It operates by passing the effluent through a jet into a region of high vacuum, where differential diffusion of the solute and carrier gas molecules effects separation. It can be used with a full range of column types and has the advantage of sweeping away dead volume between the end of the GC column and the separator entrance.
Johnson noise Thermal noise in electrical components originating from the thermal excitation of electrons. It occurs particularly in feedback resistors of electron multipliers.
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kilo
K kilo One thousand prefix.
kinetic energy The energy of a particle deriving from its motion. Relevant to fragmentation in tandem MS where collisional activation is taking place.
kinetic energy release The translational kinetic energy of fragments arising from decomposition of a metastable ion.
kinetic isotope effect The presence of an isotopic atom in a molecule can lead to changes in a reaction rate; this is called a kinetic isotope effect. The effect is measured by the ratio of the two rates of reaction.
kinetic method A procedure used to obtain the relative measurement of gas-phase proton affinities of molecules. Tandem MS is employed to determine the ratio of the abundances of the two product ions from a gas-phase dimeric species. Thus the ion
Kinetic method for determining relative proton affinities
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kinetic shift [A ……H+…...B] is dissociated by CID and the ratio of the intensities of the product ions [AH]+ and [BH]+ is measured. A calibration set of the ratios for species of known acidities is used to determine the value for the experimental species and the assumption is made that the rates of dissociation for the two process are equivalent. While changes in entropy are ignored in the original description of this procedure, recent implementations take these into account.
kinetic shift The additional energy required in excess of that for threshold formation of the fragment ion, so that the fragmentation will occur within the timescale imposed by the measuring instrument, e.g. within an EI source residence time, which is typically 1 x 10-5 seconds.
Kingdon trap An early ion trap, developed in 1923, that uses a purely electrostatic field for ion trapping. It forms the basis for the Orbitrap mass spectrometer.
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lab-on-a-chip
L lab-on-a-chip The ever-increasing need to miniaturise the methods for handling and reacting substances (see nanotechnology) has led to the development of chips etched with channels and reservoirs which can be used to control the flows of separate fluids and their reactions with each other. The chips can be based on materials like silicon, quartz, glass, or silicon rubber. In MS, the fluid flows can be made to exit though a small aperture and, with the application of an appropriate electrical charge, be ionised by a nanoelectrospray process.
Lab-on-a-chip
ladder sequencing In determining the amino acid sequence of a peptide or protein, or the nucleotide sequence of an oligonucleotide, the process whereby single amino acid or nucleotide residues are excised sequentially from either the C or N terminus. Mass spectrometric measurement of the mass of the diminishing chain allows the identities of the residues removed to be determined. The sequential removal of the terminal groups can be achieved by enzymatic or chemical means. 89
lamellar magnets lamellar magnets Electromagnets suitable for modern double focussing magnetic analysers made of alloys designed to permit fast scanning with high magnetic fields in a strictly reproducible manner.
laminar flow A non-turbulent mode of fluid flow in which the fluid moves in a series of parallel layers, with no interaction between the layers.
laser An acronym standing for light amplification by stimulated emission of radiation. The laser is an optical device that produces an intense beam of monochromatic and coherent photons. This is used in MS for the desorption of molecules from condensed phases, for the fragmentation of preformed ions and for the formation of ions from analytes embedded in an appropriate matrix (see MALDI). Common laser types include gas lasers, chemical lasers, excimer lasers, solid-state lasers, dye lasers and semiconductor lasers.
laser-activated microprobe mass analysis (LAMMA) A microanalytical technique designed to detect and characterise the elemental composition of small sections of surfaces. A visible range laser is focussed, with a microscope, on the area of the section to be analysed. This is followed by a pulsed high-energy laser beam to desorb and ionise the elements present in that area. Areas as small as 0.5 micron can be defined. The ions so formed are analysed with a TOF mass spectrometer.
laser desorption
Schematic of the LAMMA 2000 scanning instrument. University of Dusseldorf, Germany
The production of a molecular species in the gas phase from a condensed phase by the application of a pulse of energy provided by a laser. For a fragile organic molecule to survive intact it is important that the process occurs in as short a time as possible. Lasers are successful as they can be fired in pulses of a few nanoseconds duration.
laser desorption ionisation As for laser desorption but with the simultaneous formation of ions. 90
laser dissociation laser dissociation Ion fragmentation induced by the effect of a pulse of photons from a laser. It has been used in the structural determination of ions held in ion traps of both the Paul and the Penning types.
laser ionisation The interaction of a laser photon beam with a desorbed molecule can lead to its ionisation. The use of two separate lasers, one to desorb and the second one to ionise, has been reported in studies aimed at understanding the processes involved.
laser microprobe mass analysis see laseractivated microprobe mass analysis laser pulse The duration of the laser pulse can have a significant effect on the efficiency of ionisation. Differences in the duration are found between UV and IR lasers.
leak detector Small mass spectrometers with direct gas inlet systems and an EI source are used for detecting leaks in pneumatic systems.
library 1. A collection of mass spectra, most frequently arising from EI, used to identify unknown compounds by comparison. Some general libraries contain several hundred thousand spectra, such as the NIST and Wiley collections, while others are more specialised containing smaller numbers of spectra of specific classes of compounds, such as steroids, drugs and pesticides. See also mass spectral database 2. A collection of amino acid sequences of proteins used for studying protein structures.
library search The application of a pattern recognition algorithm to obtain the closest matching spectra from a library of mass spectra to that measured for an unknown compound. Most commonly applied to EI spectra, although attempts are being made to apply the technique to tandem mass spectra. 91
LIFT TOF/TOF LIFT TOF/TOF A commercial term for a tandem TOF/TOF mass spectrometer. LIFT is a device by which the potential energy of the ions in the CID region is raised to permit high-energy collisions.
limit of detection (LOD) The smallest amount of an analyte that can be detected above the background signal. It is frequently accepted as the concentration that gives a peak height three times that of the background noise (s/n = 3). Often referred to as the detection limit.
limit of quantitation (LOQ) While it has been defined as for LOD but with a factor of ten times the average noise level, other suggestions include a more rigid statistical approach such as a value of ten standard deviations above a mean blank value. It is, in the last analysis, the least quantity of an analyte which can be determined with a defined precision.
linear ion trap (LIT) A development of the classical annular Paul ion trap in which ions are trapped in the space between the four rods of a quadrupole analyser. They are mass-selectively ejected axially from one end of the trap or, orthogonally, through slits in the sides. As with the Paul trap, multiple stages of tandem MS can be performed with this analyser. The linear ion trap alleviates the problem of limited ion storage capacity in three-dimensional ion traps. Schematic of a radial linear trap
linear range In quantitative analysis, the range of concentration of an analyte over which the analytical signal is directly proportional to the analyte concentration. When the linear range is exceeded, the addition of more analyte will increase the analyte signal, but not in a directly proportional manner.
linked scan A scan performed in a double focussing magnetic sector analyser where the electrostatic analyser deflection voltage and the magnetic field are linked to a defined function such as a constant ratio. See B/E, E2/V scans 92
lipidomics lipidomics The term used to describe studies of the nature and role played by lipids and families of lipids, especially with regard to their biological significance. An important aspect of the analysis of complex mixtures of lipids is provided by MS.
liquid chromatography (LC) The form of chromatography in which the stationary phase is packed into a column through which a moving phase of solvent is passed. The differential effects of retention by the stationary phase coupled with elution by the moving solvent phase cause different substances to separate as they pass down the column. Stationary phases include surfaces which attract solutes by ionic attraction, hydrogen bonding and ligand bonding, as well as those with defined pore sizes which will separate mixtures according to molecular size. The relatively large particle sizes ensure that the liquid can flow through with little or no pressurisation, unlike HPLC in which the smaller particle sizes and better packing require that the liquid flow be pressurised. See also HPLC
liquid chromatography/mass spectrometry (LC/MS) Analysis of the eluting liquid from a liquid chromatography column by direct linking to a mass spectrometer ion source. Ion sources which operate at AP are ideally suited for LC systems. The current range of sources can ionise nearly all classes of organic molecules.
liquid secondary ionisation Ionisation taking place in a condensed phase by the action of a focussed beam of atoms or ions, as in FAB ionisation.
liquid secondary ionisation mass spectrometry (LSIMS) A closely related ionising process to FAB in which a beam of energetic ions, as opposed to atoms, is focussed on the analyte-matrix mixture.
lithium adduct Adducts of the type [M + Li]+ can be formed in mass spectra by adding a small amount of a 93
lock mass lithium salt to the sample, or by preparing lithium salts of long-chain carboxylic acids and other organic molecules. The adducts can provide molecular weight information and produce product-ion spectra with good structural information.
lock mass Over a period of time, the m/z calibration of some analysers can drift. This can be corrected by introducing and detecting an ion of known m/z value and correcting the electrical parameters of the analyser to keep this ion in focus. In common use with magnetic sector and TOF analysers especially when accurate mass measurement is being obtained.
Lorentzian peak The signal output from ICR trap analysers comprises peaks which are Lorentzian in shape compared to the usual Gaussian peak arising from a quadrupole or magnetic analyser. A typical peak shape is shown in the figure.
losses, neutral see neutral loss scan low-energy collision Lorentzian peak
In CID of ions with an inert gas, multiple collisions at ion energies in the region of 10 to 200 eV. These energies are typically achieved in ion traps and triple quadrupole analysers.
lower limit of detection (LLOD) see limit of detection lower limit of quantitative analysis (LLOQ) see limit of quantitation low-mass cut-off A fundamental consequence of the Mathieu equations for a quadrupole ion trap is that in a CID experiment a fragment ion with an m/z of less than approximately 33% of the value for a precursor ion will not be retained in the trap and will not be detected.
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m/e
M m/e see m/z m/z The dimensionless quantity used in MS to describe the detected ion, where m is the mass of the ion in unified atomic mass units (u) and z is the number of charges on the ion, whether positive or negative. The term is used to label the abscissa in a mass spectrum. m/z is often referred to as the mass-tocharge ratio and other common units for this quantity include dalton and thomson.
magic bullet A matrix for FAB ionisation comprising a 5:1 w/w mixture of dithiothreitol and dithioerythritol.
magnetic field strength (H) A quantity, distinct from the magnetic flux density, that is measured in amperes/m (SI units) or Oersteds. It is related to the magnetic flux density (B) by the relationship B = µH where µ is the magnetic permeability of the medium. 95
magnetic flux density (B) magnetic flux density (B) The magnetic field, measured in Tesla (the SI unit). 1 Tesla equals 10,000 Gauss (the older unit).
magnetic sector analyser A single focussing analyser in which ions pass through a magnetic field that is perpendicular to the ion direction of motion. The ion experiences a force which will incline it to take up a circular path. The mnemonic Fleming’s Left Hand Rule reminds how the force, current and magnet field interact. The equation of motion is: Magnetic sector analyser. Photograph by Tony Mallet
r2 = 2Vm/B2ze The radius of curvature (r) depends on the mass-tocharge ratio for a fixed accelerating voltage (V) and magnetic field strength (B). e is the charge on an electron and z is the number of charges on the ion.
magnetron motion One form of induced motion of an ion in a Penning trap. This is a presessional motion of an ion along a path of constant electrostatic potential. The frequency of magnetron motion is normally much smaller that that of cyclotron motion.
MALDI see matrix-assisted laser desorption/ionisation Mascot A commercial software programme which uses MS data to identify proteins from primary sequence databases.
mass accuracy A figure which defines the range of uncertainty over which the measured m/z value has been measured. This is the primary determinant of the possible elemental compositions which fit this figure. See accurate mass
mass-analysed ion kinetic energy spectrometry (MIKES or CAD-MIKES) In a reverse geometry magnetic sector instrument, ions selected in the magnetic sector which then dissociate in the field-free region between the 96
mass analyser magnet and the electrostatic sectors can be analysed according to their kinetic energy release. The accelerating voltage V and the magnetic field B are fixed and the electrostatic sector is scanned. The width of the detected peaks is related to the kinetic energy release involved in the product ion formation. This technique can produce differential spectra for closely related isomeric species. In contrast to the IKES technique, MIKES permits following the ion fragmentation in the source beyond the first generation.
mass analyser Once ions have been formed and introduced into the vacuum, they are subjected to electrical (DC and/or RF) or magnetic fields. Their motion under these conditions is a function of many parameters but all include the mass-to-charge ratio. Ions can be ejected from the analyser one m/z at a time or can be detected and measured, while trapped in the analyser.
63.0
62.0
61.0 %HV
1.66 E
1.62 E
1.58 E
Mass-analysed kinetic energy (MIKES or CAD-MIKES). Widening of metastable peaks analysed by high-voltage scan (left) and electric sector scan MIKES (right). Reproduced from Cooks R.G., Beynon J.H., Caprioli R.N. and Lester G.R., ‘Metastable Ions’, Elsevier, NY (1973), with permission
mass and electron parity see nitrogen rule mass calibration see calibration mass chromatogram The display of a series of spectra, acquired while a sample was introduced through a chromatographic system, can be shown as the sum of the intensities of all the ions, i.e. the TIC signal. Alternatively, only a single ion or a range or combination of ions can be chosen. The latter traces are extracted ion mass chromatograms. See selected ion chromatogram diagram
mass defect The accurate mass of any nucleus is less than the sum of its constituent protons and neutrons. This is due to the mass component in the binding energy of the atom. The difference is known as the mass defect.
mass discrimination The efficiency with which an analyser can transmit a range of m/z ions tends to diminish with increasing mass. This is most noticeable in quadrupole analysers. High m/z ions are also less 97
mass, exact efficiently detected by most detectors (see SQUID).
mass, exact see exact mass mass excess The negative value of the mass defect.
mass fingerprinting see mass mapping mass-flow-dependent detection Detection in which the signal is proportional to the change of mass with time, giving peak areas that do not vary as the flow rate of the mobile phase is altered, in contrast to a concentration-dependent detector. ESI is a concentration-sensitive technique over part of its optimum flow rate range, whereas APCI and GC/MS tend to be mass-flow dependent. However as the efficiency of ionisation in spray sources varies with the flow rate, solvent composition and hydrophobicity of the analytes, it is hard to separate all these parameters for any one experiment.
mass gate see ion gate mass limit The upper limit of m/z values that can be focussed by the analyser onto the detector.
mass mapping 1. An older term for a mass chromatogram. 2. A process for determining the RMM of peptide fragments by MS and comparing these with the calculated values from a protein sequence database, to lead to an identity for the protein.
mass measurement error The m/z range over which an accurate mass can be determined for an ion determines the number of possible elemental composition fits. These are also limited by application of valency rules, known elemental composition etc. Mass measurement error is usually measured in ppm.
mass range The range over which a mass spectrometer analyser can operate. Quadrupole, Paul and linear 98
mass resolution ion traps tend to be limited to upper m/z values around 4000. Penning FTICR and TOF analysers have mass limits that can extend this to well over 200,000 but there is a resolving power trade-off at high m/z values.
mass resolution A measure of the separation between two peaks. For overlapping singly-charged peaks of equal height, resolution is the mass difference between the two peaks when the overlap between them is at a given fraction of the peak height. In the diagram, if this is 10% of the peak heights, the resolution is for the 10% valley method. Other definitions include the 50% valley method, where this is 50%, and the FWHM method where the width of a single peak at half its height is divided into the mass. See full width half maximum height
Mass resolution
mass-selective axial ejection The removal of ions or a range of ions of defined m/z values from an ion trap by the application of appropriate electric fields.
mass-selective instability scan mode In quadrupole analyser traps, the applied RF and DC voltages are ramped to permit the ejection of ions of increasing m/z values one at a time from an ion population stored in the trap. This was an important development in the process of making a working ion trap capable of producing spectra comparable to sector instruments.
mass spectral database The fingerprint nature of EI spectra has led to the production of a number of libraries of such spectra. Unknown compounds can be searched against these collections using pattern recognition programmes. Attempts are also in progress to apply similar techniques to tandem product-ion spectra from soft ionisation methods such as ESI. Aston (1919)
B
mass spectrograph A mass spectrometer in which all ions transmitted through the analyser are focussed along a plane and in which, in earlier times, a photographic plate could be used to record their impact. In more recent designs, this is achieved by using a focal plane detector. The early instruments devised by
1 E Source
Photographic plate
An early mass spectrograph designed by Aston in 1919
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mass spectrometer Aston and those with Mattauch-Herzog geometry use this design.
mass spectrometer An instrument which measures the ratio of mass to the number of charges of ions produced from elements and compounds. It is also of value in performing fundamental studies of the properties of gaseous ions.
mass spectrometric immunoassay A technique in which molecules of biological interest are captured from a complex mixture by exposure to a surface-bound antibody. The resulting complex is released and analysed for the captured molecule using MALDI TOF MS, the non-covalently bound molecule being desorbed and ionised. See also SELDI
mass spectrometry The science of the application of the use of a mass spectrometer.
mass spectrometry/mass spectrometry see tandem mass spectrometry mass spectroscopy Alternative (and discouraged) term for mass spectrometry, which should not be used to avoid any confusion with optical techniques.
mass spectrum A plot of the abundance of an ion against its massto-charge ratio. The former is usually normalised to 100% for the most abundant ion formed.
mass-to-charge ratio see m/z mass unit see unified atomic mass unit (u) match index A parameter which describes the overlap between a calculated and an experimental mass spectrum, generally as part of a program of spectral library searching which suggests chemical identity for an unknown compound by comparing the pattern of EI spectra and observed isotopic abundances. 100
Mathieu equation Mathieu equation The behaviour of an ion in a quadrupolar electric field, like that produced in a quadrupole analyser or in a Paul ion trap, is described by the Mathieu equations. These describe the motion of an ion in a quadrupole analyser or ion trap by defining what RF and DC signals will permit the passage of an ion through a quadrupole analyser or maintain it in an ion trap without it colliding with any surface present. One form of these is shown in the figure.
Mathieu stability diagram A two-dimensional representation of regions of DC and RF voltages applied to quadrupole filters and ion traps which illustrate whether an ion of a defined m/z value will be retained in the device.
matrix 1. A material in which the analyte is dispersed to effect ionisation from a condensed phase, especially in FAB or MALDI. In FAB, the matrix is generally a liquid such as glycerol and in laser techniques it is usually a solid, such as 2,5dihydroxybenzoic acid. The matrix serves several purposes. It acts as an intermediate in the transfer of energy to the sample, so that in laser techniques, the laser is tuned to the wavelength of the matrix and does not have to be tuned for individual analytes. It also serves to separate the analyte molecules from each other, minimising the formation of clusters. 2. An extraneous material in which an analyte is contained, such as urine, soil, water or air.
au =
8zeU z mω 2 r02
qu =
4zeV mω 2 r02
These Mathieu equations describe the conditions where an ion of mass-to-charge ratio m/z will be able to pass through a quadrupole filter. Uz is the DC potential, V the peak-to-peak RF voltage, ω is the frequency of the latter signal, r0 is the distance between the rods, au and qu are related to the x and y co-ordinates of the ion path
matrix-assisted laser desorption/ionisation (MALDI) Introducing the analyte molecule in very low concentration (< 1 part in 1000) into a crystalline matrix produces a sample from which efficient ionisation can be obtained by the action of photons from a laser. The matrix is chosen for its ability to absorb the wavelength of the laser emission and to co-crystallise with the analyte. The initial action of the laser is to desorb high-energy particles from the matrix and these, in a secondary action, ionise the analyte by protonation (or cationisation) and deprotonation. The intermittent action of the laser makes this technique ideally suited to a pulsed analyser such as a TOF.
Matrix-assisted laser desorption/ionisation (MALDI). The Thermo Scientific MALDI LTQ Orbitrap. Courtesy of Thermo Scientific
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matrix effects matrix effects Any influence exerted by components of the matrix in which the analyte is present which affect the signal being measured, will lead to erroneous results. The matrix can be a biological fluid or tissue, soil, water, air, and so on. The simultaneous presence of substances which may or may not be ionised in a mass spectrometer source can alter significantly the ionisation process. This is a major reason why direct and simple mixture analysis is difficult to perform on a mass spectrometer. In MALDI MS and FAB MS, the crystalline matrix with which the analyte is mixed can affect the degree of ionisation. In quantitative analysis using GC/MS or LC/MS, it is important to establish that signal measurements are not being affected by the simultaneous elution of ion-suppressing or ionenhancing material from the column, also called a matrix effect.
matrix-matched calibrators Calibration standards prepared in matrix blank extract, which compensate for specific matrix effects.
Mattauch-Herzog geometry A magnetic sector analyser mass spectrometer in which the design of the electrostatic analyser and the magnetic analyser is configured to bring all transmitted ions onto a plane. These can then be detected by a focal plane detector or, as in the case of the original mass spectrograph, by a photographic plate.
maximum entropy Electrospray mass spectra containing multiply charged peaks can be deconvoluted use maximum entropy algorithms, which transform the spectrum into a neutral-based spectrum. Overlapping ion signals arising from mixtures are deconvoluted and improved mass resolution is often obtained.
McLafferty rearrangement
McLafferty rearrangement
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An ion fragmentation characterised by a rearrangement within a six-membered ring system. The most usual configuration is for a radical cation formed by EI to undergo the transfer of a γhydrogen atom to the ionisation site through a ring system as shown here. The distonic radical cation
McLeod gauge so formed can break up by radical-site-induced (α), or charged site-induced fragmentation as shown in the figure.
McLeod gauge A mechanical vacuum gauge employed chiefly as a primary calibration standard for other gauges. A known volume of gas at unknown pressure is captured in a glass bulb and compressed into a small, closed capillary of known volume by raising the mercury level. The original pressure is calculated using Boyle’s law. It is generally used from 1 Torr to 10-4 Torr.
mean free path For an ion, this is the average distance it can travel between collisions. At a rough estimate, an ion of mass 200 u will have a mean free path of 10-5 m at 10-3 Torr and 450 m at 10-9 Torr. For efficient transmission, analysers need to operate at low pressures.
membrane introduction mass spectrometry (MIMS) The direct analysis of an aqueous solution, a flowing liquid, or a gaseous sample by EI or CI can be achieved by passing the liquid past a semipermeable membrane, usually consisting of silicone polymer tubing. The analyte diffuses through the membrane, which acts as the interface between the sample and the mass spectrometer. The technique has been applied to the analysis of volatile compounds in air and water and for process monitoring.
mesomeric effect The electron-releasing or electron-withdrawing properties of a functional group in a molecule based on resonance canonical structures is called the mesomeric effect of that group. In the case of ion fragmentation, this effect will promote or prevent certain pathways of reaction taking place.
Membrane introduction mass spectrometry (MIMS). Reproduced from ‘Membrane Introduction Mass Spectrometry: Trends and Applications’, R. C. Johnson, R. G. Cooks, T. M. Allen, M. E. Cisper, P. H. Hemberger, Mass Spectrometry Reviews, 2000, 19, 1-37 © 2000 by John Wiley & Sons, Inc.
metabolic pathway The specific chemical reactions taking place in the metabolism of defined classes of natural products such as carbohydrates, lipids etc.
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metabolism metabolism Metabolism covers all forms of drug or natural product modification, synthesis or decomposition that can take place within an organism. It includes catabolism and anabolism.
metabolomics A recently introduced term to describe the study of the complete metabolism of all low-molecularweight substances in one organism.
metastable ion An ion which fragments in the field-free regions of multisector magnetic analysers and can be examined by appropriate electrostatic and magnetic field scans.
methane Methane, CH4, is frequently used as a moderating or reactant gas in CI sources.
method limit of detection see limit of detection micro One millionth part.
microbore In order to benefit from the increased sensitivity of ESI at low flow rates, miniaturisation of the components of the HPLC separation system is common. Microbore HPLC columns have internal diameters of about 1 mm and use solvent flows of 10-50 µl/min.
microchannel plate detector A regular array of 100 or more miniature electron multipliers arranged in a plane. They are used in MS as focal plane detectors in Mattauch-Herzog geometry analysers and in TOF analysers. See also continuous dynode electron multiplier
microelectrospray A form of low-flow electrospray with flow rates below 1 µl/min, but not as low as those used in nanoelectrospray.
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microorganisms microorganisms The direct analysis of microorganisms by MALDI TOF MS is a well-developed technique. It depends on examining the fingerprint pattern of the proteins detected in order to distinguish between different organisms.
micro-reversibility A description of the succession of small steps involved in protein folding that contribute to the final three-dimensional shape of the molecule. MS is one of several techniques employed in these studies.
microscan A commercial implementation of the operation of an ion trap which seeks to prevent space charging effects. It consists of a chain of several steps occurring sequentially, such as ion injection, isolation, excitation, and analysis.
microscopic states The individual bond movements involved in the total mechanism needed to describe the steps by which a protein folds.
micro-total-analysis system An alternative term for lab-on-a-chip.
milli A one thousandth part.
mixture analysis While unseparated mixtures are often difficult to measure by MS and can exhibit significant matrix effects, the employment of tandem MS permits the isolation of individual molecular ions and their analysis in subsequent product ion scans. See also matrix effect
molarity The concentration of a compound expressed in moles/litre.
molar mass The mass in grams of one mole of a substance with atomic masses based on the unified atomic mass scale. See also relative molecular mass 105
mole mole An SI unit defined as the quantity of particles of anything including atoms, ions and molecules equivalent to the number found in 12 g of carbon12 atoms. This quantity is the Avogadro number.
molecular beam mass spectrometry A technique in which the sample is a beam of molecules of narrow molecular weight distribution. It has been used for the analysis of flames, plasmas and clusters.
molecular ion An ion formed from the original molecule by electron ionisation, by the loss of an electron, or by addition or removal of an anion or cation. The latter have sometimes been referred to as quasimolecular ions.
molecular mass see relative molecular mass (RMM) molecular weight The original term for molecular mass. It is loosely used to describe integral, average and accurate molecular masses.
monoisotopic molecular mass The molecular weight calculated using only the atomic weights of the most abundant isotope of the elements present. This can be precise or integral in character.
moving belt interface An early implementation of an HPLC/MS interface. The removal of the LC solvents was achieved by depositing the eluate onto a slowly moving and heated continuous Kapton belt which was driven into the ion source through slots and areas of efficient pumping. The analyte molecules were desorbed from the belt by flash desorption or, in later versions, by surface ionisation techniques such as FAB.
MSn Multi-stage product ion generation by successive isolation of the precursor ion from the molecular ion or from a set of product ions, followed by CID 106
MS/MS fragmentation to produce new product ions. This experiment can only be performed in ion traps where tandem MS in time is possible. For experiments where n > 4 the overall response diminishes rapidly.
qx
.908
qx
.908
qx
.908
qx
.908
qx
.908
MS/MS see tandem mass spectrometry multichannel plate detector see microchannel plate detector multicollector Stable isotope ratio MS uses multiple Faraday cup detectors for the simultaneously determination of the abundances of the ions of the isotopic species being studied. This provides the necessary precision for this type of work.
multidimensional protein identification technology (MudPIT) A technique for protein identification which avoids the use of two-dimensional gel electrophoresis. A protein complex is digested with trypsin and the whole peptide mixture is separated with a twodimensional micro HPLC system as shown in the figure. This consists of a strong cation exchange column directly attached to a reversed phase column. Stepwise elution of peptides from the first column using increasing salt concentrations is followed at each step by a reversed phase elution from the second column. The peptides sequences are determined by tandem MS.
MSn. Schematic of the HRI (high resolution isolation) process which is an ion isolation technique. Courtesy of Thermo Scientific
multiphoton ionisation Ionisation in which more than one photon is absorbed by the molecule.
multiple collision conditions see low-energy collision multiple excitation collisional activation (MECA) In FTICR MS, a technique for achieving ion dissociation by periodic ion excitation through application of an on-resonance RF signal followed by cyclotron motion relaxation by multiple collisions.
Multidimensional protein identification technology (MudPIT)
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multiple reaction monitoring (MRM) multiple reaction monitoring (MRM) see selected reaction monitoring (SRM) multiplier see electron multiplier multiturn analyser
Multiturn analyser. For a review see M.Toyoda et al, J. Mass Spectrom, 2003, 32, 1125-1142
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A mass spectrometer in which the ions pass through several analysers, several times. This has been demonstrated for multiple electrostatic and TOF analysers and can enhance the resolving power of the instrument. It is also referred to in the literature as a Multitum analyser.
nano
N nano The prefix for 10-9, as in nanometer.
nano-assisted laser desorption/ionisation (NALDI) A proprietary term for an ionisation technique that is related to MALDI. Samples are deposited on a nanostructured target plate comprising dense arrays of silicon nanowires for matrix-free laser desorption/ionisation. The nanostructures are designed to absorb the laser energy to bring about desorption of the sample. The ions are usually analysed in a TOF mass spectrometer giving mass spectra with very low chemical background. The technique is particularly suitable for small molecules.
Nano-assisted laser desorption/ionisation (NALDI). Courtesy of Bruker
nanochromatography Liquid chromatography typically using flow rates of 10-1000 nl/min, for which columns of internal diameter 10-150 µm are employed.
nanoelectrospray An electrospray technique that uses flow rates at the low nl/min level. These are usually achieved using a fused silica capillary with a narrow tip a 109
nanospray few µm in diameter. At these low flow rates, droplet formation occurs more easily, generally dispensing with the need for sheath gas and producing a more stable spray.
nanospray Commonly used in place of the term nanoelectrospray. It was originally a commercial term coined (as NanoSpray) as a trade name for nanoelectrospray. A nanoelectrospray source mounted on a Qtof mass spectrometer (New Objective Picoview) Photograph by Tony Mallet
nanotechnology The fabrication and use of devices on the nanoscale, that is, at dimensions at the nanometre level.
natural isotopic abundance The isotope abundances of an element in its natural form, as found in nature. For carbon, there are 3 natural isotopes 12C, 13C and 14C, with abundances of 98.89, 1.11 and 1.2 x 10-12%, respectively. The natural stable isotopic contributions of the various elements in an ion produce isotopic distributions in its mass spectrum, resulting in a series of isotope clusters at each nominal mass.
nebulising gas A gas that is added to the ion source to assist the formation of charged droplets from the liquid spray during LC/MS. The gas serves the additional purpose of transporting the droplets from the capillary towards the mass spectrometer. Nitrogen is the most common nebulising gas. Also referred to as sheath gas.
negative ion An ion with a net negative charge, known also as an anion.
negative ion chemical ionisation (NICI) The form of CI that produces negative ions.
neutralisation reionisation mass spectrometry A technique for studying transient species in which mass-selected ions are neutralised in a collision chamber by charge exchange with a neutral gas, or 110
neutral loss by dissociation. The neutral species are then reionised by collisional ionisation in a second collision chamber and the mass spectra of these newly ionised species are measured.
neutral loss The loss of an uncharged radical, a molecule, or a fragment of a molecule on the dissociation of an ion, such as the loss of ammonia from an ionised amino acid.
Neutral loss
neutral loss scan Many classes of compounds lose a common neutral fragment during fragmentation. In a type of tandem MS scan, this common difference between the m/z values of the precursor and product ions is analysed by scanning both mass spectrometers together with a constant mass offset. This technique is often used as a marker for the presence of a particular functionality in the compound. For instance, neutral loss of 98 Da (for phosphoric acid) is used in proteomics analyses to signal the presence of a phosphopeptide, phosphoprotein, or a phosphorylated amino acid residue.
Nier-Johnson geometry A double focussing mass spectrometer in which the electrostatic sector is positioned before the magnetic sector. The electric and magnetic fields have deflection angles of /2 and /3 radians, respectively. Both mass and energy focussing occur at a single common point, at which the collector slit is positioned. Also called EB geometry.
Nier-Johnson geometry. Reproduced with permission from ‘Introduction to Mass Spectrometry’, J.T. Watson and O.D. Sparkman, © 2007 John Wiley & Sons, Ltd
nitrogen generator A device for producing nitrogen gas from air, used as an alternative to nitrogen cylinders, or boil-off from a pressurised liquid nitrogen Dewar. Separation from the other air gases is generally accomplished using a permeable membrane. A secure supply of clean nitrogen is essential for the operation of most AP ion sources.
nitrogen rule The nominal molecular weight of a compound will have an even-number value if there are no nitrogen atoms, or an even number of nitrogen atoms,
Nitrogen generator. Courtesy of In House Gas Ltd
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nominal molecular mass present in the molecule. This holds for compounds containing C, H, O, P, S, Si, or halogen atoms. Even-electron fragment ions containing an even number of nitrogen atoms occur at odd-number m/z values. Conversely, if there are an odd number of nitrogen atoms, the nominal molecular weight will be an odd number and even-electron ions containing an odd number of nitrogen atoms occur at even-number m/z values.
nominal molecular mass The mass of a molecule or ion calculated using the integral masses of the most abundant isotopes of each element present, such as 1 for hydrogen, 12 for carbon, 14 for nitrogen, 16 for oxygen and 79 for bromine. A given nominal mass can correspond to several molecular formulae. For molecules it is referred to as the nominal molecular mass or nominal molecular weight. For bromomethane (CH3Br), the nominal molecular mass is 94, but the electron ionisation mass spectrum will show m/z values at 94 and 96 corresponding to the 79Br and 81Br isotopes of bromine.
non-classical ion A hypervalent carbonium ion such as CH5+, as opposed to the tri-coordinated carbenium ion, such as C2H5+.
non-covalent interaction Molecules and ions can associate by non-covalent attractions, including hydrogen bonds and van der Waals bonding. Studies of these species, including large entities such as protein assemblies, can be performed by ESI MS.
normalisation In the mass spectrum, the abundance of the most intense peak is assigned 100 units (100%) and the abundances of the remaining peaks are adjusted in proportion. This facilitates the comparison of spectra from different compounds.
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octapole
O octapole A device containing eight rods used as an ion guide to focus divergent beams of ions and as a storage device to accumulate ions before transfer to another part of the system. RF voltages and a DC offset voltage are applied to the rods. Also called an octupole.
odd-electron ion Radical cations, such as those formed in EI, contain an unpaired electron. These can fragment by loss of a radical leading to an even-electron cation or by loss of a neutral species, the product ion still being a radical odd-electron species.
off-axis detector In order to prevent non-specific signals from a detector arising from the impact of neutral species, the detector is placed off the ion beam axis and the ions are deflected by a charged metal surface. One alternative approach is to use curved analyser configurations in which no linear path for the ions is present.
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off resonance off resonance see SORI oligonucleotide A sequence of up to 20 nucleotides joined by phosphodiester bonds.
oligopeptide A sequence of 2 to approximately 30 amino acids linked by peptide bonds.
oligosaccharide Oligosaccharides are composed of a number of simple sugar (carbohydrate) molecules linked through one or more oxygen substituents to form linear and branched chains. They are essential components of the glycosylation of proteins, lipids and other classes of biological molecule.
onium ion A hypervalent species containing a non-metallic element such as the methonium ion CH5+. It includes ions such as oxonium, phosphonium, and nitronium ions.
open-shell An element with an incomplete set of valence shell electrons. Only the inert gases exist with a full set of electrons in the valence shell and other elements will complete the set by covalent bonding with other elements.
Orbitrap
Orbitrap. Courtesy of Thermo Scientific
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A novel ion trap analyser based on the Kingdon trap, originally described in 1923. The trapping field is electrostatic, with no RF or magnetic component. The ions are trapped in a cylindrical container which has a central spindle-like electrode and cycle around and along this central electrode. Detection can be performed, as in an FTICR trap, by monitoring the frequency of motion (axial oscillation) of the ion packets inside the trap, or by the application of a mass-selective instability supplementary RF field, by ejecting the ions through an aperture and detecting them externally. The instrument has a very high claimed resolving power up to 200,000 and mass ranges up to 50,000 u. Combined with a linear or Paul ion trap, complex tandem MS scans can be performed.
O-ring O-ring A leak-free join between flanged parts of the mass spectrometer is maintained by the use of elastomer O-rings. Most common O-ring material is limited to use from below 250° to 350°C. Above this temperature metal (gold) rings are required.
ortho effect The interaction between substituents oriented ortho, as opposed to para and meta, to each other on a ring system, can create specific fragmentation pathways. This permits the distinction between these isomeric species. The diagram shows a case in which only the ortho isomer can undergo the rearrangement.
Ortho effect
orthogonal 1. A linear stream of ions from a quadrupole analyser or any other source can be subjected to a deflecting pulse which makes a section of the stream move at right angles to the original direction of motion. In MS, the deflected ion beam is passed down a TOF analyser and the m/z values of the ions present are measured. This process has the advantage that all the deflected ions are moving in synchrony at the start of the TOF process, leading to improved resolving power. 2. Orthogonal alignment of API sprays to the acceptance aperture of mass spectrometers as found in ESI and similar sources. This prevents much neutral material from entering the analyser.
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paper chromatography
P paper chromatography The original chromatographic separations were performed using a filter paper stationary phase and having a solvent move through the paper as the mobile phase.
parent ion An ion that reacts to form a product ion, generally by CID, unimolecular decomposition or by modification of the total number of charges. On account of its gender-specific nature it is now referred to as precursor ion.
parent-ion scan see precursor-ion scan particle beam interface
Particle beam interface
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A device for coupling the eluate from an LC column to a mass spectrometer. This is designed to be the liquid-phase equivalent to GC/MS and provide EI/CI spectra. The eluate is passed through a nebuliser to form droplets, which are completely desolvated by passing through a heated momentum separator to remove the vapour and carrier gas from the analyte molecules. This beam of solute
pascal (Pa) particles (the particle beam) enters the ion source where it is vaporised by striking the hot source walls, then ionised by conventional EI or CI.
pascal (Pa) The SI unit of pressure. 1 Pa = 10-5 bar and 133.32 Pa = 1 Torr.
pattern recognition 1. A technique for structure elucidation based on the classification of mass spectra by representing the peaks and intensities as points in multidimensional space. A reference library, or training set, is used to establish the positions of the ions for comparison with the unknown spectrum. 2. In proteomics, pattern recognition is used to compare protein profiles and identify differences, which can lead to the identification of disease markers.
Paul trap An ion trap in which the ions are manipulated by a three-dimensional quadrupole field. An RF voltage is applied to a cylindrical ring electrode to trap the ions in circular orbits near the centre of the trap. Two end-cap electrodes are positioned either side of the ring electrode. As the RF voltage is increased and a small RF voltage is applied to the end caps, the ion orbits become unstable as the m/z values increase sequentially, and they move towards the end caps, where they pass through holes to reach the detector. Also called a cylindrical ion trap or quadrupole ion trap (QUISTOR).
Paul trap schematic
peak 1. A region in a mass spectrum where there is a concentration of ion signal, corresponding to an m/z value. 2. A chromatographic peak is a region in a chromatogram corresponding to the elution of a particular compound.
peak intensity The signal measured for the detected ion in a mass spectrometer. The preferred term for a set of ions in a spectrum is ion abundance.
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peak matching peak matching A technique for exact mass determination of an ion in a magnetic sector mass spectrometer. One or more reference ions of known m/z value and the target ion are introduced simultaneously into the ion source. The accelerating voltages of the two ions are adjusted so that they reach the detector at the same time, resulting in overlapping peaks. The m/z value of the target ion can be determined from the ratios of the accelerating voltages.
peak parking A technique for increasing the analysis time of a particular chromatographic peak eluting from the column, using variable column flow rates. When the target peak enters the mass spectrometer, the HPLC flow rate is reduced immediately to increase the time available for further measurements, such as tandem studies. At the end of the chromatographic peak, the flow rate is returned to its original value.
peak stripping A data manipulation procedure for removing interfering peaks or separating interfering peaks. In common use in ICPMS and GDMS elemental analyses.
Penning gauge A cold cathode ion gauge in which a stream of electrons under the influence of a high voltage ionises residual gas molecules which are allowed to impinge on a cathode under the influence of electric and magnetic fields. The current which flows is a function of the pressure. This type of gauge can be used from 10-3 to 10-10 mbar
Penning ionisation Penning gauge. Courtesy of INFICON Limited, Liechtenstein
The spontaneous ionisation of gaseous species by collision with internally excited, metastable species.
Penning trap An ion trap in which ions are trapped by a magnetic field and travel in circular orbits perpendicular to this field. Electric fields applied to trapping plates prevent the ions from escaping axially. Upon application of an RF field, the ions 118
peptide are moved to wider orbits and pass by receiver plates which measure the induced (or image) current caused by the ion frequencies of motion. These frequencies are inversely proportional to the ion mass. This trap does not destroy the ions, which can be retained for long experiments. See ICR and FTICR
peptide A compound composed of at least two α-amino acids linked by amide bonds formed from the amino group of one peptide and the carboxylic acid group of another. Longer peptides are termed proteins when they are biologically active. A simple dipeptide is shown in the figure.
Peptide
peptide sequencing The peptide bond can be broken at three places and the residual charge can be found at either the N-terminus or the C-terminus. The diagram here shows the six possible fragment ions which are referred to by the letters a, b, c, x, y, z. They are often written with a subscript number to indicate at which point in the peptide chain the fission has taken place. With high-energy CID, other fission products can be observed with bond breaking at both peptide and side chain bonds and these are named with the letters w and v. See also immonium ion and internal fragment
The three peptide bonds which can break on CID with the letters indicating the three N-terminal and the three C-terminal resulting ions
per cent valley resolution see mass resolution perfluorokerosene A mixture of perfluorinated alkanes, often added as a mass calibrant in EI and CI MS. It gives a series of well-spaced ions across the mass range up to above m/z 900 (EI) and m/z 800 (NICI).
perfluorotributylamine A compound often added as a mass calibrant in EI MS, as it gives a series of well-spaced ions across the mass range up to m/z 614 in positive mode and m/z 652 in negative mode.
per mil The unit representing parts per thousand, indicated by ‰. Also known as permil, per mill and per mille. 119
phenylium ion phenylium ion The ion at m/z value 77 which is often produced in the mass spectra of compounds containing a phenyl group as shown in the diagram.
phosphopeptide
Phenylium ion
A peptide containing at least one phosphorylated amino acid residue. Many proteins contain phosphorylated residues and are digested with enzymes to produce smaller phosphopeptides which are analysed by MS to determine the phosphorylation sites. Only serine (Ser), threonine (Thr), tyrosine (Tyr) and, more rarely, histidine (His) residues are commonly phosphorylated.
photodiode array detector (PDA) see diode array detector photodissociation The dissociation of an ion or molecule following excitation by photon impact. It is used to help elucidate fragmentation mechanisms, often in place of CID, and the most common method uses laser excitation. In an ion trap, ions can be held for extended periods of time, permitting longer photon-ion interaction times.
photographic plate An early form of detector in which the plate is positioned at the focal plane and all ions are detected simultaneously, giving the full mass spectrum. Ions of the same m/z value are focussed to the same position on the plate.
photoionisation The ionisation of an atom or molecule following excitation by photons.
photomultiplier A device for converting light into an electric signal. Photons strike a cathode which emits electrons that are accelerated towards a dynode, which they strike and produce a greater number of electrons. These are directed towards a series of dynodes, producing a cascade effect to generate an amplified signal. The electrons are directed towards a phosphorescent screen where they are converted into photons. They are used in detectors, 120
photon-induced dissociation (PID) such as the Daly detector, where the first step is electron impact on a phosphor to release photons. This signal is then amplified by a photomultiplier.
photon-induced dissociation (PID) see photodissociation photon stop A device to prevent photons (light) impacting on a Daly type detector
pico The prefix for a factor of 10-12. Symbol p. As in 5 picograms, or 5 pg.
Pirani ion gauge A vacuum gauge employing a heated wire, the resistance of which is a function of the residual gas pressure. Used for pressure measurement in the range from atmospheric pressure to 10-2 mbar.
planar chromatography see thin layer chromatography
Pirani vacuum gauge, Courtesy of MK instruments
plasma 1. An ionised gas, containing a freely moving mixture of charged particles, neutral particles and electrons, typically in the form of a gas cloud. It is formed by the application of heat, light or electrical energy to a gas, such as a microwave discharge. It is used as the ionising source in an ICPMS instrument. 2. In APCI, the needle which produces the corona discharge forms a plasma to produce ions which react with the analyte molecules, inducing ionisation.
plasma desorption see californium desorption
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Cf
pneumatically assisted electrospray The use of a gas flow to assist the formation of droplets from the liquid spray during electrospraying. Conventional sources have a concentric gas capillary around the liquid capillary and the most common gas employed (the nebulising gas) is nitrogen. This system can cope with higher liquid flow rates of up to 2 mL/min. 121
point detector point detector A detector which focusses the ion beam to a point so that the ions arrive individually and sequentially.
polymerase chain reaction (PCR) An in vitro process used to amplify DNA or oligonucleotide sequences without using living organisms. It is a three-step process with each step conducted at a different temperature. The two strands of the DNA molecule are separated by heating, small pieces of DNA (primers) corresponding to one end of the target sequence are added and the polymerase enzyme starts at the primer and copies the whole sequence of each strand. Around 1 million copies can be produced in a few hours.
portable mass spectrometer A self-contained mass spectrometer that can be easily moved and operated in the field. Current applications include forensic work (drugs, explosives), the detection of chemical warfare agents in the battlefield, the analysis of pollutants in water by underwater MS, and space research.
positive ion An ion with a net positive charge, known also as a cation.
positive ion chemical ionisation (PICI) The form of CI that produces positive ions. Portable mass spectrometer. Courtesy of ICx Technologies, Inc., IN, USA, www.griffinanalytical.com
positive rays An early term used to describe the stream of positively charged particles generated in a vacuum tube that moved towards the cathode, in the opposite direction to electrons (known then as cathode rays).
post-acceleration detector (PAD) A detector in which the ions are accelerated after mass analysis, to increase the detection efficiency. Ions of higher mass have less impact velocity than those of lower mass under the same conditions, so they produce fewer electrons when they hit the detector plate. Increasing the momentum by accelerating the ions counteracts this reduction in efficiency. 122
post-source decay (PSD) post-source decay (PSD) The decay of ions in the flight tube of a TOF instrument after full acceleration, before they reach the reflectron. The product ions from this fragmentation have the same velocities as their precursor ions but have different kinetic energies. The TOF is unable to resolve the precursor and product ions in linear mode, since they reach the detector at the same time. In reflectron mode, the ions are resolved according to their kinetic energies, so can be detected separately to yield product-ion spectra. The design of the reflectron is important as a linear arrangement has to be scanned over a number of m/z ranges to ensure all the fragment ions impinge on the detector’s surface. This applies to metastable dissociation and to CID. See also curved field reflectron
post-translational modification (PTM) A structural change to a protein that occurs after the formation of all peptide bonds, that is, after translation. Examples include acetylation, phosphorylation, glycosylation and the formation of disulphide bonds.
potential energy diagram A graphical representation of the way atoms and molecules interact and react with each other, in which the free energies of the reactants are plotted along the course of the reaction.
precision The closeness of multiple measurements on the same sample. These may not be accurate.
precursor ion An ion that reacts to form a product ion, generally by CID, unimolecular decomposition or by modification of the total number of charges. Also known as parent ion, a term which is not recommended.
Potential energy diagram. Reproduced from Mass Spectrometry: Principles and Applications, E.de Hoffmann and V. Stroobant, p74, © John Wiley & Sons, Ltd
precursor-ion scan A scan in which all of the precursor ions of a selected product ion are identified. In a triple quadrupole instrument, the third quadrupole transmits the product ion and the first quadrupole scans the mass spectrum. Only those ions which 123
precursor-ion spectrum fragment in the collision cell to the selected product ion are recorded. This type of scan is not directly possible on a TOF or ion trap.
precursor-ion spectrum The spectrum produced by recording the m/z values of the precursor ions of a product ion or a set of product ions.
primer A short fragment of DNA consisting of a few nucleotides, which is used in PCR. The primer is complementary to one end one of the duplex DNA strands and binds to it to initiate the copying process.
principal components analysis (PCA) A mathematical procedure for reducing the complexity of multidimensional data sets, while retaining the majority of the original variability. The first principal component accounts for the maximum variability possible and each successive component accounts for as much of the remaining variability as possible. The technique helps to visualise patterns within the data and is used in pattern recognition.
principal ion The most abundant ion in an isotopic cluster.
probability based matching (PBM) A type of search algorithm for matching unknown mass spectra against those in a library of reference spectra. It employs a pre-search stage to determine the relative importance of the peaks, followed by a reverse search that compares the unknown spectrum to every spectrum in the library and assigns a match probability.
probe inlet
Probe inlet. Photograph by Tony Mallet
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A type of inlet for introducing solid samples directly into the ion source, used especially for involatile or thermally labile compounds. The sample is loaded on the probe tip then introduced to the source via a vacuum lock. The sampling rate can be controlled to some extent by controlling the heating rate.
product ion product ion An ion that is formed by the reaction of a precursor ion, generally by CID, unimolecular decomposition or by modification of the total number of charges. Also known as daughter ion, a term which is not recommended.
product-ion scan A scan in which all of the product ions of a selected precursor ion are identified. In an ion trap, the precursor ion is retained in the trap while all other ions are rejected, then it is subjected to CID. In a triple quadrupole and other instruments with a collision cell, the first analyser selects the precursor ion and the second analyser, after the collision cell, detects the product ions.
product-ion spectrum The spectrum produced by recording the m/z values of the product ions of a precursor ion.
profile mode A way of recording the peaks in a mass spectrum, by plotting continuously the observed ion current against the m/z ratio or time. Each peak is displayed as a curve, the individual points on the curve corresponding to the ion count, or ion signal intensity at that point. Algorithms are generally employed to find the centroid mass and assign a discrete m/z value to the peak. Also referred to as continuum mode.
profile mode spectrum A mass spectrum recorded in profile (or continuum) mode, displayed as a trace containing a series of peaks. Electrospray mass spectra are often recorded this way. Algorithms are employed to convert the peaks to the centroid or digitised form, displayed as m/z values versus intensities.
prompt fragmentation see in-source CID protein A biologically active compound, also referred to as a polypeptide, comprising chains of α-amino acids linked by amide bonds formed from the amino group of one peptide and the carboxylic acid group of the next. Up to 20 different amino acids are
A three dimensional representation of the amino acid chain in a protein
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protein chip involved, with a typical protein containing 200300 in total. After the proteins have been synthesised in vivo, the structures of the peptide groups are often changed by PTM.
protein chip A microfabricated device for detecting and measuring small amounts of proteins and for studying their interactions with other biomolecules or small molecules. Capture agents such as monoclonal antibodies are immobilised on a chip and the protein is trapped and removed from its matrix, such as blood, then released for analysis. Protein interactions are studied by immobilising a peptide, drug or other compound as the trapping agent and only those proteins that interact with the immobilised molecule will be trapped. Also referred to as a protein array.
protein, ladder sequencing see ladder sequencing protein, mutation The modification of a protein in which one or a few residues are replaced by other residues, either during its natural translation or deliberately by site-directed mutagenesis, as a consequence of mutations in the DNA. Such changes can affect the properties of the protein if they occur in an active region of the protein sequence.
protein, phosphorylation see phosphopeptide protein sequencing The determination of the order of the amino acid residues in a protein.
proteolysis The degradation of a protein to produce smaller fragments. It is used to break down proteins into peptides for easier analysis and is usually accomplished with a variety of high specificity enzymes such as trypsin, chymotrypsin, endoproteinase Lys-C and endoproteinase Glu-C. Trypsin cleaves the peptide chain on the C-terminal side of arginine and lysine residues. Chymotrypsin cleaves peptides at the carboxyl 126
proteomics side of phenylalanine, tryptophan and tyrosine residues. Lys-C hydrolyses amide or ester bonds at the carboxylic side of Lys residues, whereas Glu-C cleaves at the carboxyl side of aspartic and glutamic acid residues. Proteolysis is also a natural biochemical process used to regulate the amounts of cellular proteins.
proteomics The identification and detection of expression of all proteins in an organism and the determination of their structures, interactions and functions, as well as their responses to cellular and external influences.
proton The hydrogen ion, H+. In physics, proton refers to the subatomic particle with a single positive charge and a mass of 1.673 x 10-27 kg and a charge of 1.602 x 10-19 Coulomb.
proton addition The addition of a hydrogen atom with a single positive charge to a molecule or ion. It is a common process used in the ionisation of molecules in techniques such as ESI.
proton affinity (PA) For a molecule M, it is the negative value of the enthalpy change in the reaction measured at 298K: M + H+ = [M + H]+. Higher values indicate that the proton is more tightly bound. PA is inversely proportional to the gas-phase basicity.
protonated molecule A positive ion formed by the addition of a proton to a molecule, designated [M + H]+. It is often referred to as a protonated molecular ion, a pseudomolecular ion, or a quasi-molecular ion, none of which are recommended.
proton mass A value of 1.673 x 10-27 kg.
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proton transfer proton transfer The exchange of a proton between an ion and a molecule or another ion. It is used in processes such as CI, APCI, MALDI and ESI to ionise molecules and is also used to determine the charge state of highly charged molecules via ion/molecule reactions. Proton transfer reactions (PTR) are also involved in the fragmentation of multiply charged peptides and proteins using an experimental arrangement closely related to ETD.
pseudomolecular ion An ion formed by the addition of a proton or another ion to a molecule, or by the loss of a proton from a molecule. This term is not recommended. An [M + H]+ ion formed by the addition of a proton to the molecule should be called a protonated molecule. An [M - H]- ion formed by loss of a proton should be called a deprotonated molecule. Other ions wrongly labelled pseudomolecular ions include [M + NH4]+, [M + Na]+ and [M + Cl]-.
pulse count signal The most sensitive ion detection method, in which each ion striking the detector creates an individual pulse. The count rate is limited by the recovery time (dead time) of the detector between pulses but is usually in the range from 1 to 106 counts per second for electron multipliers.
pulsed ion extraction see delayed extraction pyrolysis mass spectrometry
A pyrolysis MS instrument (Courtesy SS Scientific Limited, UK)
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The controlled thermal degradation of samples to give smaller fragments that are analysed by MS, providing a chemical fingerprint of the sample. The process is carried out in a vacuum or an inert atmosphere such as nitrogen to eliminate oxidation reactions which complicate product analysis. Heating can be accomplished using Curie point wires to give reproducible temperatures. The technique is used for complex samples such as synthetic polymers, rubbers, biopolymers, humic substances, organic matter, microbes in a clinical environment and fossil fuels.
Q
Q Q Common symbol for a quadrupole analyser to which both DC and AC voltages are applied.
q Common symbol for a quadrupole array to which only a RF voltage is applied and which then acts as a focussing device applicable to a range of m/z value ions. Often used to indicate the collision chamber of a tandem mass spectrometer.
qu Parameter in the Mathieu equation. See Mathieu equation
quadratic field reflectron A reflectron or ion mirror in which the electric field strength varies as the square of the distance from the entrance. It provides an approach to the problem of reflecting ions with a wide range of kinetic energies to a focus.
quadrupolar axialisation In FTICR MS, a technique for concentrating the ion packet into a small volume by converting 129
quadrupolar field magnetron motion to cyclotron motion followed by collisional damping.
quadrupolar field A field generated by four poles or rods, such as in the quadrupole ion trap or the quadrupole, that traps the ions and acts as a mass filter. By manipulating the potentials applied to the rods, the field is adjusted to allow ions of specific m/z values to be focussed, stored, or ejected.
quadrupole A device containing four precisely parallel conductors onto which DC and RF voltages can be applied to create a quadrupolar field and which can act to focus, store or analyse ions. Also referred to as a transmission quadrupole.
quadrupole ion storage trap (QUISTOR) see Paul trap quadrupole ion trap (QIT) see ion trap quadrupole time-of-flight mass spectrometer (QTOF) A tandem mass spectrometer in which the ions from a quadrupole analyser pass through a collision chamber and the product ions are then orthogonally accelerated into a TOF analyser for detection and mass measurement.
quantitative analysis Quadrupole time-of-flight mass spectrometer (QTOF). Exact Mass LC/MS/MS: Waters® Xevo™ QTof quadrupole time-offlight MS system. Image courtesy of Waters Corporation. www.waters.com/msms
The use of MS for quantitative studies is widespread. The complexity and difficulty in ensuring that all the instrumental parameters can be set to produce identical effects on all occasions has meant that the use of internal standards is virtually obligatory for acceptable precision.
quartz torch The quartz assembly in which the inductively coupled argon plasma is maintained in an ICPMS system.
quasi-equilibrium theory A theoretical treatment of the thermodynamics of ion decomposition. The theory assumes that, because the ionisation process takes place over a 130
quasi-molecular ion time frame (10-16 sec) shorter than that required for a molecular vibration, excess internal energy will be distributed equally over all bonds in the molecule. Fragmentation by bond breaking will therefore be independent of the original site of ionisation and depends only on the structure of the molecule itself.
quasi-molecular ion An ion which is closely related to the molecular ion, in which ionisation has taken place by addition or loss of a charged species, such as a protonated molecule [M + H]+, a deprotonated molecule [M - H]- or a cationised molecule such as [M + Na]+. This term is no longer in common use.
Quasi-equilibrium theory. Morse curves for electron ionization. A vertical transition is observed if the interatomic distances have no time to adjust. The opposite is represented by the oblique line. Ionization can lead to higher energies, including the excited electronic state. Reproduced from Mass Spectrometry: Principles and Applications, E.de Hoffmann and V. Stroobant, p 276, © John Wiley & Sons, Ltd
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radial ejection
R radial ejection In a linear ion trap, ion trajectories are governed by axial and radial components of the trapping field. They can be ejected from this trap in a direction perpendicular to the central axis of the trap, called radial ejection, or parallel to the axis, called axial ejection. In a Paul trap, ions are only ejected axially through the end caps.
radiation cooling The release of excess energy from an ion following EI, by the emission of photons in the UV and visible ranges.
radical anion An anion containing an unpaired electron that is denoted by a superscript dot after the charge, as in C6H6– • . It can contain more than one charge and more than one unpaired electron and can be a molecular ion or a fragment ion.
radical cation A cation containing an unpaired electron that is denoted by a superscript dot after the charge, as in 132
radical ion C2H5+ • . It can contain more than one charge and more than one unpaired electron and can be a molecular ion or a fragment ion.
radical ion A positive or negative ion containing an unpaired electron that is denoted by a superscript dot after the charge, as in C6H6– • or C2H5+ • . It can contain more than one charge and more than one unpaired electron and can be a molecular ion or a fragment ion.
radiocarbon dating A technique used to date organic materials based on the decay of the naturally occurring isotope carbon-14, which is measured by AMS. The halflife of carbon-14 is 5730 years but measurements have to be adjusted for the continuous production of carbon-14 from the impact of cosmic rays on the Earth’s atmosphere.
radionuclide A radioactive form of an atom that undergoes radioactive decay, such as carbon-14. Also referred to as a radioisotope.
rate constant A measure of the rate of a chemical reaction, symbol k. It can be expressed in terms of the concentrations of the reactants. For example, in the reaction of A with B: rate = k[A]m[B]n where [A] is the concentration of A, [B] the concentration of B, and m and n are the powers to which the concentrations are raised. In tandem MS, whether or not a product ion can be observed is defined by the kinetics of the fragmentation process.
Rayleigh stability limit As the solvent evaporates from the charged droplets produced by electrospray, the droplets begin to shrink in size while the charge remains constant. This increases the Coulombic repulsion forces between the charges until, close to the Rayleigh stability limit, these forces become
The bursting of a charged droplet as it evaporates and the surface charges exceed the Rayleigh limit. Photo courtesy Nature, 1994, 367, p.21
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reaction coordinate stronger than the surface tension holding the droplets together. At this stage, the droplet undergoes Coulomb fission into a series of smaller droplets which may also undergo the same shrinkage and fission processes in a cascade process until solvent-free gas-phase ions are produced. The Rayleigh stability limit (qR) is defined as qR= 8π(ε 0 γ R 3) 1/2 where ε0 is the permittivity of the vacuum, γ is the surface tension and R is the droplet radius.
reaction coordinate A one-dimensional coordinate that is used to represent the progress of a chemical reaction along the reaction pathway. The coordinate is generally plotted against the free energy of the reaction. See potential energy diagram
reagent ion An ion used to react with a neutral analyte molecule to produce analyte ions in a CI source. The reagent ion can be positive or negative and it can produce protonated or deprotonated analyte molecules, adduct ions or molecular ions.
rearrangement
Rearrangement of a tropylium ion
The formation of new bonds between atoms in an ion, followed in some cases by the elimination of a neutral fragment. Rearrangements can involve hydrogen migration only, or can form bonds between atoms other than hydrogen (skeletal). They can be useful for interpreting mass spectra. See also McLafferty rearrangement
recombinant protein A protein produced by a genetically modified organism which has had a defined DNA sequence inserted into its genome to encode a particular protein with a known function. This can be an effective way to produce relatively large quantities of a protein.
recombination energy The energy released during the addition of an electron to an ion, the inverse of the ionisation energy. 134
reconstructed ion chromatogram (RIC) reconstructed ion chromatogram (RIC) A chromatogram that has been reconstructed from the recorded mass spectra, showing the intensity of one or more given m/z signals, or logical combinations of m/z signals, as a function of time or scan number. See also selected ion chromatogram (SIC)
reconstructed total-ion-current chromatogram A chromatogram that has been reconstructed from a series of consecutive mass spectra, by plotting the sum of the intensities of all the peaks in a mass spectrum against the scan number. Peaks in the chromatogram correspond to scans of interest where compounds have been eluting above the background signal.
reference ion An ion of known composition formed from a reference compound to assist in the identification of ions of unknown structure.
reference material see certified reference material (CRM) reflectron An electrostatic ion mirror in a TOF analyser which reflects ions passing down the flight tube back towards a detector. With the reflectron switched off, the ions travel towards a detector behind the ion mirror to give a low resolution spectrum. With the reflectron switched on, ions of identical m/z that were travelling towards the ion mirror at different kinetic energies become focussed as they are reflected, leading to higher resolution. Some instruments have more than one reflectron, further increasing the resolution. Also known as an ion mirror.
A TOF analyser showing the ion flight path through the electrostatic mirror.
reionisation The ionisation of a neutral species, formed by neutralisation of an ion. See neutralisation reionisation MS
relative intensity The intensity of an ion in a mass spectrum, relative to that of the base peak. The base peak intensity is 135
relative ion abundance usually set to 100% and all other ions have intensities below this value. The relative intensities represent the ion abundances in the mass spectrometer.
relative ion abundance The relative abundances of ions in the mass spectrometer. The ion for which the signal is the most intense is arbitrarily assigned 100% abundance in the mass spectrum.
relative molecular mass (RMM) The sum of the relative atomic masses of the atoms in a molecule, calculated for specific isotopes based on the unified atomic mass unit. So, the atomic masses of hydrogen, nitrogen and oxygen are set to 1, 14 and 16, respectively and the relative integral molecular mass of 4pyridinecarboxaldehyde (C6H5NO) is 107 [(6 x 12) + (5 x 1) + (1 x 14) + (1 x 16)].
remote fragmentation see charge-remote fragmentation repeller A metal plate, placed in an EI source, to which a low DC voltage is applied in order to promote the transfer of newly formed ions into the mass spectrometer.
residual gas analyser (RGA) A type of mass spectrometer, typically based on a quadrupole mass analyser, used for the detailed gas analysis of vacuum systems. It is often used in the semiconductor industry to check for contamination and for process control. When combined with the introduction of trace amounts of helium, it is also used for leak detection.
resolution see mass resolution or resolving power resolving power
Resolving power
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A measure of the ability of the mass spectrometer analyser to separate two ions of different, but defined, m/z value. For two overlapping singlycharged peaks m1 and m2 of equal height, the resolving power is defined as m1/Δm, where m1 is
resonance the m/z value of one ion and Δm is the mass difference between m1 and m2 such that the two peaks are resolved with a defined interpeak valley. In the diagram, if h is 10% of the peak heights, then the method is called the 10% valley method. Other definitions include the 50% valley method, where h is 50%, and the FWHM method. For two adjacent peaks at m/z values of 200.00 and 200.05 separated by a 10% valley, the resolving power is 200.00/0.05 = 4000.
resonance The oscillation of an atom, ion or molecule in an ion trap that is induced by excitation with energy of a particular frequency.
resonance-enhanced multiphoton ionisation (REMPI) A two-stage photoionisation process which separates the excitation and ionisation steps. Initially, the neutral species is excited by multiphoton absorption using a tuneable dye laser that is set to an intermediate electronic state. This is followed by laser ionisation and the resulting ions are typically analysed in a TOF mass spectrometer. REMPI gives a marked increase in ionisation cross section compared with nonresonant photon absorption. The overall ionisation process is soft and leads to few if any fragment ions.
Resonance-enhanced multiphoton ionisation (REMPI). Courtesy of Robert Donovan, University of Edinburgh, UK
resonance ion ejection The ejection of an ion from a Paul ion trap by the application of an auxiliary RF voltage that matches the ion’s secular frequency, that is, the frequency at which the ion oscillates in the trap. The auxiliary voltage is applied through the end cap electrodes. When ion resonance occurs, the ion trajectory increases with time and it will be ejected if the amplitude of the resonance signal is sufficiently large. Otherwise, the ion will undergo resonant excitation.
resonant excitation The excitation of ions in an ion trap by resonant irradiation at either one or both of the axial and radial secular frequencies. This is carried out in order to increase the kinetic energies of the ions and to eject unwanted ions from the trap. 137
retro Diels-Alder retro Diels-Alder
Retro Diels-Alder fragmentation, the radical cation formed by EI can fragment in two ways, depending on radical site or charge site initiation
A multicentered ion fragmentation which is the reverse of the classical Diels-Alder reaction employed in organic synthesis that forms a cyclic alkene by the cycloaddition of a substituted diene and a conjugated diene. In the retro reaction, a cyclic alkene radical cation fragments to form either a diene and an alkene radical cation or a diene radical cation and an alkene. Depending on the substituents present in the original molecule, the more stable radical cation will dominate.
reverse geometry The set up of a double-focussing mass spectrometer where the magnetic sector is followed by the electric sector. Symbol BE.
reverse library search A method for comparing an unknown mass spectrum with a mass spectral library, in which the library spectra are compared to the unknown spectrum. The spectra are searched sequentially to see if they contain the m/z values in the unknown spectrum, considering only those peaks in the library spectra with relative intensities above a certain value.
RF coil In an ICPMS source, an RF signal is fed through a tightly wound coil to produce a strong magnetic field. A plasma torch is positioned within the coil and the electrons and ions formed in the plasma are accelerated towards the magnetic field to form a stable plasma. If the RF field is switched off, the plasma will collapse.
RF-only mode A mode of operation of a quadrupole mass spectrometer in which the DC field is switched off and only the RF field is applied. This makes the instrument operate as a high mass filter, passing all ions present. This mode is typically used for ion injection, for example in a hybrid quadrupole-TOF instrument.
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rings and double bond equivalents (RDBE) rings and double bond equivalents (RDBE) A measure of the degree of unsaturation of an organic compound, also known as rings plus double bond equivalents, or index of hydrogen deficiency. It is related to the number of rings and double bonds in a molecule and is described by the formula: DBE = 1 + [0.5 x ∑Ni(Vi-2)] N is the number of atoms of element i and Vi is the valence. So for cyclohexane (C6H12), DBE = 1 (one ring) and for benzene (C6H6) DBE = 4 (3 double bonds + 1 ring).
rod One of a set of parallel cylindrical electrodes, or poles, in a quadrupole mass spectrometer or other mass filter such as the hexapole or octapole. In the quadrupole mass spectrometer, opposite rods are connected electrically to DC and RF voltages to control the ion trajectories.
rotary pump A type of mechanical pump which uses a revolving action to pump out gases and maintain a vacuum. The required use of lubricating oil limits the attainable pressure to about 1 Pa for singlestage pumps and 0.1 Pa for two-stage pumps, so they are used as forepumps to reduce the pressure for diffusion and turbomolecular pumps which cannot operate until these pressures have been reached.
roughing pump Any type of mechanical pump used as a forepump for the initial evacuation of a system, to reduce the vacuum to 0.1 Pa or below, at which pressure a high-vacuum pump such as an oil diffusion pump can be operated.
RRKM theory Rice, Ramsperger, Kassel, Marcus theory. A theory used to calculate fragmentation reaction rates and predict fragmentation patterns. 139
Rydberg ionisation Rydberg ionisation Molecules with an electron affinity can be ionised by species which have been excited to a Rydberg state, having electrons with energy dispersion of a few meV. When they transfer an electron to the analyte molecule a radical Rydberg excited anion is formed with negligible internal energy and hence little potential for fragmentation.
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saddle-field FAB gun
S saddle-field FAB gun A device to produce fast atoms from an inert gas such as argon or xenon, which are accelerated onto the FAB target to promote ionisation. A beam of high-energy ions at about 8 kV is passed through a cloud of thermal electrons trapped by an electric saddle field. The ions undergo resonance electron capture to form the fast atoms.
sampler cone see cone sandwich method A technique for preparing a sample for MALDI analysis. A droplet of matrix solution is applied to the sample stage and allowed to evaporate rapidly. A drop of the analyte solution is placed on top and this too is dried. A second droplet of matrix solution is finally applied to the sample and when this has dried the MALDI analysis takes place.
Saddle Field Gun. Photograph by Tony Mallet
saturation Most detectors employed in MS have a limit to their response to intense beams of ions and are said to saturate. Equally, ion sources have limited 141
scan ionisation capability and will cease to respond linearly when excess material is introduced.
scan One operation of a scan law function of the analyser to produce a measure of ion intensity/abundance as a function of time or m/z.
scan law The relationship between the time period of a scan and the range of m/z values being transmitted. While sector analysers tend to be scanned exponentially, most other analysers use linear scans.
scanning analyser In MS, an analyser which is regularly cycled to permit transmission and detection of ions of a range of m/z values. In an FTICR MS trap, the entire packet of frequencies detected is processed by a fast FT process to produce the m/z vs. abundance spectrum.
scanning microprobe matrix-assisted laser desorption/ionisation The need for direct in situ analysis of target molecules in biological tissues has led to the development of small well-defined laser pulses for use in LDI and MALDI. Typically a nitrogen laser can be operated with a spot size of 7 microns. The laser is rastered across the sample surface in a grid pattern to produce a two-dimensional image of selected ions across the sample.
scanning speed Analysers are scanned with a regular cycle time from low to high m/z or vice versa. Quadrupole analysers tend to be scanned linearly in mass while a magnetic analyser is scanned exponentially to provide peaks of equal width throughout the mass range. Fast scan speeds are needed when a mass spectrometer is linked to a fast chromatographic system and TOF analysers are currently among the best for this.
scroll pump A mechanical roughing vacuum pump which operates with no oil and can be used to back high 142
secondary electron vacuum turbomolecular pumps when very clean environments are important.
secondary electron The impact of ions, photons or electrons on a solid surface can lead to the emission of secondary electrons. This phenomenon is important in mass spectrometer detectors.
secondary ion mass spectrometry (SIMS) Bombarding a solid surface with a stream of highenergy ions causes the elements exposed on the surface to become ionised and amenable to mass spectrometric analysis. Continual sputtering of the surface material permits depth profile analysis to take place. In practice, the efficiency of ionisation of the ejected material is very low and one modification has been to bombard the surface with neutral atoms and to ionise the sputtered material with a secondary ion source such as an electron beam or laser-derived photons. This latter technique is abbreviated to secondary neutral MS (SNMS).
Secondary ion mass spectrometry (SIMS). A schematic representation of a SIMS instrument. Reproduced with permission from J.C. Vickerman, Chem. Brit. 969 (1987)
sector mass spectrometer This usually refers to a mass spectrometer with magnetic and electrostatic sector focussing devices.
secular frequencies Ion trajectories in the ion trap are characterised by two components, or secular frequencies, corresponding to the axial and radial motions of the ion that are caused by the trapping field. One or both of these frequencies can be used for resonant excitation of the ions to increase their kinetic energy, remove unwanted ions, and eject selected ions.
selected ion chromatogram (SIC) A chromatogram for one or more m/z values or ranges that has been extracted from the TICC, showing the intensity of that signal as a function of time or scan number.
selected ion flow tube mass spectrometry (SIFT MS) A technique for the qualitative and quantitative
The lower panel shows the TIC for a succession of scans while the upper panel only records the intensity of the m/z 138 ion.
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selected ion monitoring (SIM)
Selected ion flow tube mass spectrometry (SIFT MS). Courtesy of David Smith and Patrik Spanel of Keele University, UK
determination of volatile organic molecules in gaseous samples such as breath. Ions, most frequently from an argon-air microwave device, but many other ion sources have been used, are injected into a quadrupole analyser from which a selected ion species is driven down a tube by a helium buffer gas. The analyte vapour is admitted downstream and the products of the ion/neutral reactions are analysed in a second quadrupole analyser and detected in the usual manner. Applications range from fundamental studies of ion/molecule reactions to rapid diagnosis in medicine.
selected ion monitoring (SIM) Target compound analysis, often in combination with an on-line chromatographic separation, in which the analyser is programmed to transmit one or more ions in a sequence. The selected ions are characteristic of the target analyte. This has the potential to increase the overall sensitivity of the mass spectrometer response by avoiding the time spent, in scanned spectra, on areas of the mass range where no ions of interest will be found. Also known as selected ion recording (SIR).
selected reaction monitoring (SRM) Increasingly high degrees of specificity can be achieved in the detection and analysis of mixtures by using tandem MS in which the two analysers are set to transmit only pre-defined pairs of precursor and product ions. This is the most common mode of operation in quantitative analysis in combined LC/MS. Also referred to as multiple reaction monitoring (MRM).
sensitivity The slope of a calibration curve in a quantitative analysis. Selected reaction monitoring (SRM). Quantitative analysis of Clenbuterol in human urine using SRM and H-SRM. Courtesy of Thermo Scientific
sequencing The process of determining the sequence of the individual components in a polymer such as a protein, DNA or an oligosaccharide. MS plays a leading role in the determination of the amino acid sequence of peptides.
SEQUEST A software programme developed in the 144
sheath gas University of Washington, USA, to determine peptide amino acid sequences from tandem MS data. Now a commercial product.
sheath gas see nebulising gas sheath liquid A liquid that is added to the sample spray in AP ion sources, often via a concentric capillary, to help produce a stable spray. Typical sheath liquids are aqueous acetonitrile or aqueous methanol containing traces of acetic or formic acids, although many different solutions have been employed.
shotgun protein sequencing A procedure in which a mixture of proteins is digested with an enzyme to give a mixture of peptides. Tandem MS of the unseparated mixture leads to product ion spectra from which overlapping amino acid sequences can be extracted and deconvoluted and significant partial sequences of the parent proteins can be described. From these the probable original proteins can be deduced by database searching. See also bottomup protein identification
shot noise Noise caused by the randomness in ion arrival time at the detector. It is proportional to the number of ions arriving at the detector in a given time interval.
sigma bond cleavage If EI takes place at a single C-C bond in a molecule, the radical cation can fragment at that bond leading to one charged product ion and one radical species, as shown in the diagram. When the choice is between small and large alkyl cations the latter always predominate in spite of Stevenson’s rule.
Sigma bond cleavage
signal-to-noise ratio (s/n) The ratio of the intensity of an ion signal to that of the noise. It has been used to determine the LOD and LOQ and to calculate the precision and accuracy with which the analyte can be quantified.
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simulated ion trajectory algorithm (SIMION)
simulated ion trajectory algorithm (SIMION) A commercial optics simulation program which has become an essential tool for the design of analysing and focussing devices in the development of mass spectrometer instruments.
single photon ionisation A very soft ionisation method which uses a vacuum UV photon source working at wavelengths around 120 nm. Mass spectrometry with this technique is popular for the analysis of small molecules such as aliphatics and residual gases in the atmosphere. To be contrasted with the resonance-enhanced multiphoton ionisation (REMPI) technique which is more appropriate for aromatic compounds.
size exclusion chromatography see gel permeation chromatography skimmer cone see cone slow fragmentation The rate of ion decomposition is an important determinant for observing the event and detecting the product ions. Where the rates of reaction are slow, a device like an ICR analyser is important as it can keep ions under observation over extended periods of time.
sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)
Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)
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A technique for separating proteins in mixtures according to their electrophoretic mobility, which is related to their size. SDS is added to the proteins to bring about denaturation (unfolding) and confer negative charge by binding to them. Upon application of this mixture to a gel and applying a voltage gradient through the gel (electrophoresis), the proteins migrate at different rates, larger molecules having greater difficulty in passing than small ones. The positions of the proteins on the gel are visualised by the use of various stains such as Commassie Brilliant Blue or silver nitrate. In proteomic studies, protein separation is followed
soft ionisation by digestion with a tryptic enzyme. The resulting peptides are purified and characterised by MS (MALDI and/or ESI). SDS-PAGE alone is limited in the extent to which it can separate a complex mixture of proteins. It is usually combined with an initial separation along one axis through an immobilised pH gradient which separates proteins according to their pI values, which is combined with a second electrophoretic separation along a second orthogonal axis through an SDS gel which separates proteins according to size.
soft ionisation Ionisation in which a minimum of excess energy is imparted to the newly formed ion, producing little resultant fragmentation. Distinguished from highenergy ionisation, sometimes called ‘hard’ ionisation, typified by the products of EI.
sonic spray ionisation (SSI) The impact of a supersonic jet of gas onto a stream of the sample solution leads to the ionisation of the analyte. This has been used as an alternative to an electrospray API source. See also electrosonic spray ionisation
source The region of a mass spectrometer instrument in which the sample is ionised.
space charge effects There is a limit to the density of the ion population which can be held in a small volume in an ion trap, on account of the mutual repulsion between particles of identical charge. When too many ions are present, the behaviour of the ions no longer matches the accepted equations of motion and errors in m/z determination and resolving power occur.
spark source ionisation A high voltage RF current between two electrodes in a vacuum will produce sparks and a plentiful source of atoms and ions of the elements forming the electrodes. This is a common way to analyse solid samples for their elemental composition. One electrode is usually graphite and the other can be the analyte itself or a small crucible of the sample mounted in a second graphite electrode.
Spark plasma
50–100 kV 1 MHz
Sample
Vacuum
Ion current + n -- + + -
+
+
Mass spectrometer
10–20 kV
Spark source ionisation. Reproduced from J.S. Becker, ‘Inorganic Mass Spectrometry’, © John Wiley & Sons, Ltd (2007)
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spectra
spectra(l) collections and spectra library see library spectral acquisition rate The rate at which spectra are recorded, usually given as the number of scans per second or the number of spectra per second.
spectral interference see isobaric interferences spray ionisation A range of spray based methods for ionising analytes in solution.
sputtering The ejection of atoms from a surface by the impact of high-energy ions and atoms.
stability areas The areas in a Mathieu stability diagram which are defined by the parameters needed for an ion to be transmitted through a quadrupole analyser or to be maintained or ejected from a Paul or linear ion trap. See Mathieu stability diagram
stability diagram see Mathieu stability diagram stable isotope dilution assay Quantitative analysis using GC/MS or LC/MS in which a synthetic, stable isotope-substituted analogue of the target analyte is added to the original sample to act as an internal standard. The extent and purity of isotope substitution need to be as complete as possible.
stable isotope encoding The substitution of one or more stable isotopes into a molecule, with known ratios to each other and to the natural isotopic composition, provides a method for the recognition of pathways for species which arise by reaction or metabolism of the original molecule. A technique in common use in combinatorial chemistry.
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stable isotope labelling of amino acids in cell culture (SILAC)
stable isotope labelling of amino acids in cell culture (SILAC) A technique for obtaining proteins which have been labelled with stable isotope-containing amino acids. SILAC is used to obtain quantitative data on protein expression by comparing the spectra from two cell populations, one of which has been grown in stable isotope-enriched media.
stable isotope ratio analysis mass spectrometry (SIRA MS) Determination of the accurate ratios of elemental isotopic abundances in compounds by the analysis of small gaseous compounds containing the element under observation. Carbon is analysed as CO2, with EI. Permanent magnet analysers are often employed to achieve the extreme instrumental stability required together with Faraday cup detectors to provide the necessary low statistical variation in the data.
standard additions An alternative procedure for obtaining quantitative data from an assay. A range of known concentrations of the target analyte are added to the sample and a graph of the response to the amount of analyte added is plotted. The intercept of a regression line on the x axis is the concentration of the original analyte in the sample. The method relies on a linear relationship between the instrumental response and the analyte concentration and on a null signal for a sample with no analyte present. The figure shows a plot of the mass spectrometric response to successive additions of the analyte to the matrix. The intercept on the X-axis corresponds to the endogenous concentration.
Stable isotope ratio mass spectrometer DELTA V from Thermo Fisher Scientific with e− beam ion source and multiple ion collection. (Reproduced by permission of Thermo Fisher Scientific, Bremen Germany)
A plot resulting from a standard additions experiment
standard curve A plot of a mass spectrometer response to an analyte versus its concentration. It is more usual to use an internal standard (see internal standard and stable isotope dilution assay), in which case the response parameter is replaced by the ratio of analyte to internal standard responses and a calibration curve is formed. 149
static secondary ion mass spectrometry
static secondary ion mass spectrometry The application of SIMS in which only the uppermost layer of the surface under analysis is ionised.
stationary phase The material in a chromatographic separation which is immobilised and to which different analytes in the sample will have varying affinities.
stereochemistry A carbon atom with four different groups attached can exist in two distinct geometries. Such isomers are optically active but tend to respond identically in a mass spectrometer. See chiral
Stevenson’s rule In the dissociation of a sigma bond in a radical cation, there are two possible routes by which a neutral radical can be formed. The rule states that the radical having the highest ionisation energy will be formed with the charge being retained on the other entity. See sigma bond cleavage
stick spectrum see centroided spectrum stored waveform inverse Fourier transform (SWIFT) A method for applying an RF signal to a population of ions in a Penning or Paul trap which excites ions in a closely defined range of m/z values. Compared to a chirp this provides a more precise method for excitation and detection of the stored ion packet.
superconducting magnet Intense and homogenous magnetic fields can be achieved by employing superconducting coils in an electromagnet. The assembly has to be maintained at or below the boiling point of helium (4.2°K). The operation of an ICR mass spectrometer depends absolutely on being present in an intense magnetic field.
superconducting tunnel junction detector (SQUID) The impact of an ion on a superconducting 150
supercritical fluid niobium tunnel junction detector leads to a signal which reflects the energy of the particle. This device overcomes the decreasing efficiency of channel electron multipliers and other classical MS detectors for the analysis of ions of m/z over 100 kDa. The detector needs to operate at temperatures approaching 1K using cryogenics based on 4He.
supercritical fluid When a gas is subjected to a sufficiently high pressure and temperature it will become a supercritical fluid when the densities of the gas and liquid phases become identical. For carbon dioxide, the critical temperature and pressure are 31.1°C and 73.8 bar. Supercritical fluids are excellent solvents for a range of less polar compounds and they have been used as chromatographic solvents linked to MS.
Schematic of a superconducting funnel junction detector
suppression of ionisation see ionisation suppression surface-assisted laser desorption/ionisation (SALDI) The use of condensed phases such as graphite instead of a liquid matrix in MALDI permits the detection of ions in the regions of lower mass, where ions derived from the liquid matrix tend to obscure signals from molecules with RMM below 500.
surface-enhanced laser desorption/ionisation (SELDI) The use of immobilised affinity or biological binding molecules on a MALDI target to combine the specific extraction of target substances, their on-target purification and laser desorption analysis all in one site. Most commonly employed with commercial targets to analyse for proteins in biological matrices.
surface-induced dissociation (SID) The fragmentation of an ion by impact on a surface, as opposed to another gaseous molecule as in CID.
surface plasmon resonance (SPR) An optical method for measuring the refractive 151
surrogate standard index of thin layers of material adsorbed on a chip surface. A beam of light is directed at an angle to the surface on the opposite side to the adsorbed material. Some of the photons tunnel through the surface and excite plasmons on the opposite side. The net result is a reduction in the reflected light, which can be measured. The technique is used in BIA to study interactions between biomolecules, since binding of a target molecule to a compound immobilised on the surface changes the refractive index. The mass spectrometric interest arises from the use of a MALDI TOF instrument to analyse the bound biological molecules directly from the chip.
surrogate standard A molecule as similar to the analyte under investigation as possible but which is not expected to be present in the sample being analysed. It can be used as an internal standard for quantitative analysis. See internal standard and stable isotope dilution assay
sustained off-resonance irradiation (SORI) The application of a supplementary RF electric field to an ion in an ICR trap in order to induce decomposition of the ion. The frequency of the applied signal is slightly off-resonance to the cyclotron resonance frequency of the chosen ion. This activates the ion while maintaining it within the confines of the trap, and, through CID, leads to fragmentation.
SWISS-Prot database An important and extensive collection of gene sequences and their related protein structures which can be searched openly through the internet. It is now merged into the UniProt database.
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tandem accelerator mass spectrometer
T tandem accelerator mass spectrometer An accelerator mass spectrometer in which two beams of ions are transmitted in parallel, one from the sample and one from a calibration standard. Each sample has its own source and, after acceleration, is passed to its own detector.
tandem-in-space mass spectrometry A tandem MS experiment in which a collision cell is placed between two analysers, so that the three components are in different spatial locations. The first analyser transmits selected ions into the collision cell, where fragmentation occurs, and the product ions are analysed in the second analyser. This set up is suitable for MS/MS experiments but for higher order MSn studies, a series of n analysers separated by collision cells is required. A typical set up might be two quadrupole mass spectrometers, or a quadrupole and a TOF mass spectrometer, separated in each case by the collision cell.
Tandem accelerator mass spectrometer. Courtesy of Gunnar Tibell and Teddy Thornlund
tandem-in-time mass spectrometry A tandem MS experiment in which the all of the operations take place at different times within an 153
tandem mass spectrometry ion storage device such as an ion trap. Ions of chosen mass are isolated in the device and subjected to fragmentation, either spontaneous or assisted by, say, a collision gas or photoionisation. The fragments are analysed and may be selected for further fragmentations studies, with up to six sequential steps.
tandem mass spectrometry An experiment in which the product ions of a particular precursor ion (a product-ion scan), or the precursor ions of a particular product ion (a precursor-ion scan) are analysed. A third experiment, the neutral-loss scan, involves recording the precursor and product ions corresponding to the loss of a particular neutral fragment. The analyses can be tandem-in-time, using an ion trap, or tandem-in-space, using two linked analysers separated by a collision cell. Also called mass spectrometry/mass spectrometry or MS/MS.
tandem mass spectrum The spectrum obtained in a tandem MS experiment, which may be a product-ion, precursor-ion, or neutral loss spectrum.
target compound analysis The detection or quantitative analysis of specific compounds in a sample. Detection can be carried out by looking for characteristic ions in the spectrum, such as the molecular ion or particular fragment ions. It is typically carried out using a major ion, supported by several additional qualifying ions. This technique is used, for example, in forensic and environmental analysis, to look for drugs of abuse, poisons, pesticides and pollutants.
Taylor cone
Taylor cone. Courtesy of Rudy Schlaf
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In electrospray, the presence of the high voltage on the spraying capillary induces a charge distribution in the spraying solution as the positive and negative ions move apart. In positive mode, the positive ions move towards the meniscus of the liquid and the negative ions move in the opposite direction. The mutual repulsion between the positive ions eventually overcomes the surface
Tesla coil tension of the liquid and the meniscus expands forming the Taylor cone, first described by Taylor in 1964. In due course, the increasing repulsion overcomes the surface tension and droplets break away from the cone tip.
Tesla coil A transformer device used for the ignition of a gas plasma. In an ICPMS ion source, an RF generator creates a fluctuating magnetic field around an argon gas flow and the Tesla coil is sparked, producing a stream of free electrons that ionise the gaseous atoms, which, in turn, produce more electrons to give a self-sustaining ionisation process.
thermal ionisation Ionisation caused by the interaction of a substance with a heated filament or other surface, or, more unusually, by the distribution of a substance in a heated gas. Also referred to as surface ionisation.
thermal ionisation cavity A type of thermal ionisation source in which a metal crucible with a deep cavity is used to hold the sample for enhanced surface ionisation.
thermocouple gauge An ion gauge for measuring pressure in the range from 1 mTorr to about 2 Torr. It uses a thermocouple to measure the temperature of a hot wire which becomes hotter as the vacuum increases and fewer molecules are present for heat transfer.
thermospray ionisation (TSP) The ionisation of an analyte in solution by passing it through a heated capillary tube. As the liquid travels along the tube, much of the solvent is vaporised and the remaining liquid stream breaks up into droplets which are desolvated and produce ions by droplet fission (see Rayleigh stability limit). This process is known as filament-off. In a second mode known as filament-on, ionisation is assisted by a corona discharge or an electron beam which ionises molecules in the solvent that undergo subsequent ion/molecule reactions to ionise the analyte molecules.
Thermospray ionisation (TSP). Schematic of a thermospray LC-MS interface. From applications literature published by Vestec (Applied Biosystems), Foster City, CA. Reproduced with permission
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thin-layer chromatography (TLC) thin-layer chromatography (TLC) Chromatographic separation in which the stationary phase is a thin layer of fine powdered silica or reversed phase LC packing material onto which the mixture is spotted from a small drop. Elution is performed by allowing a solvent or mixture of solvents to flow up through this layer by capillary action. Colourless components can be detected by developing with a sprayed reagent or by fluorescence of a material incorporated into the thin layer which is seen by illumination with a UV lamp. The spots of separated compounds can be seen as dark areas on the TLC plate.
thioglycerol A common matrix employed for FAB ionisation. It has the advantages of being relatively involatile and long lasting in high vacuum and of producing only a few clearly characterised ions in FAB MS. It is often used in mixtures with glycerol.
thomson An alternative ‘unit’ for the term m/z, symbol Th, named after J.J. Thomson.
thresholding A technique used in data processing to diminish the background noise from the data in which data failing to reach a set minimum intensity is rejected.
tickle voltage A low-amplitude AC voltage applied to the end cap electrodes of an ion trap during excitation. This increases the ion motion between the end caps to allow fragmentation of the ions by collisions with the damping gas.
time-lag focussing see delayed extraction time of flight mass spectrometer (TOF) An instrument in which the ions are separated solely on the basis of their velocities without the application of any external force. Ions are accelerated down an evacuated flight tube at high potential (up to 30 kV), their velocities and flight times depending on the mass of the ion, so that lighter ions reach the detector before heavy ones. 156
time of flight tandem mass spectrometer (TOF/TOF) The m/z value is related to the flight time (t), the length (l) of the flight tube and the accelerating voltage (V) by the relationship: m/z = 2Vt2/l2 In a linear TOF mass spectrometer, the ions travel down the flight tube and are detected at the opposite end to the source. Resolving power can be improved by use of a reflectron, or a series of reflectrons, which reflect ions back down the flight tube.
Time of flight mass spectrometer (TOF). Qualitative Exact Mass LC/MS: Waters® LCT PremierTM XE orthogonal acceleration time-of-flight MS system. Image courtesy of Waters Corporation. www.waters.com/ms
time of flight tandem mass spectrometer (TOF/TOF) A tandem mass spectrometer consisting of two TOF analysers separated by a collision cell for MS/MS experiments.
time-to-digital converter (TDC) Ion detection in a TOF analyser relies on a TDC taking a pulse of ions striking the multichannel plate detector and translating these into a set of digitised ion counts which can be processed by the data system.
top-down protein sequencing A method for sequencing proteins and peptides which analyses intact molecules in the gas phase, in contrast to bottom-up sequencing which requires protein digestion. Multicharged ions are selected for dissociation, typically by CID, ECD, ETD or IRMPD, and the fragment ions are analysed. Alternatively, in-source CID is employed initially, sometimes followed by further dissociation. Identification of the starting compound relies on database searching, using algorithms for processing the MS/MS data.
The IM-1021-A - MagneTOFTM, courtesy of SGE
Torr A non-SI unit of pressure. 1 Torr = 133.32 Pa and 0.00133 bar.
total ion current (TIC) The sum of the ion currents of all the ions detected in a mass spectrum.
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total ion current chromatogram (TICC or TIC) total ion current chromatogram (TICC or TIC) During a chromatographic separation, the TIC measured in a series of mass spectra scanned over time is plotted against the retention time. The peaks in the chromatogram correspond to the elution of compounds, when ion current is relatively high.
transition state Transition state
An intermediate species formed as a chemical reaction or fragmentation proceeds from the reactant, or precursor, to the product as shown in the diagram. The transition state exists at the maximum of the potential energy surface for the reaction and has an equal probability of forming the reactants or products.
translational energy loss spectrometry (TES) High-energy collisions between an ion and a neutral target can lead to an alteration of the internal energy of the ion. TES is designed to obtain thermodynamic and spectroscopic information concerning the fragmentation processes. The instrumentation employs one or more electrostatic analysers, a collision chamber and, in one implementation, a reversed geometry double focussing mass spectrometer. Signals corresponding to varying energies and collision trajectories can be determined.
transmission A measure of the proportion of ions that passes through the mass spectrometer, expressed as a percentage or a ratio.
transmission quadrupole see quadrupole travelling wave A commercial implementation of a method for transmitting ions through regions of relative high pressure to perform CID and IMS separation.
triple quadrupole-linear ion trap mass spectrometer A hybrid instrument comprising a triple quadrupole followed by a linear ion trap, 158
triple quadrupole mass spectrometer permitting scans from both segments to be carried out in the same experiment.
triple quadrupole mass spectrometer A tandem mass spectrometer consisting of three consecutive sets of quadrupoles, two transmission quadrupoles separated by a third, RF-only quadrupole that acts as a collision cell. Ions are selected in the first quadrupole, fragmented in the second, and the product ions are analysed in the third.
trisector mass spectrometer A high-resolution instrument comprising three analysers, such as two electrostatic sectors separated by a magnetic sector.
Triple quadrupole mass spectrometer. Quantitative LC/MS/MS: Waters® XevoTM TQ tandem quadrupole MS system. Image courtesy of Waters Corporation. www.waters.com/msms
tropylium ion A stable cation in the form of a seven-membered ring, C7H7+, often formed from compounds containing a benzyl group. The bond between the methylene carbon of the benzyl group and the remainder of the molecule is cleaved and the benzyl ion rearranges into the more stable cyclic form with the charge delocalised around the ring, as shown in the diagram.
Trisector mass spectrometer. From applications literature published by Micromass UK Ltd, Manchester, UK, and reproduced with permission
tryptic digest A mixture formed by the hydrolysis of a peptide or protein, or a mixture of these, using the enzyme trypsin. Cleavage of the peptide chain occurs on the C-terminal side of arginine and lysine residues to give a series of peptides which can be identified by sequencing or mass mapping to lead to identification of the original protein. The technique is used extensively in proteomics. C7H7+, a tropylium ion
tuning Adjustment of the operational parameters of a mass spectrometer, specifically the voltages of the ion source, mass filter and detector to produce optimum peak intensities, resolution or peak shape. It is often accomplished using standard compounds such as perfluorotributylamine or decafluorotriphenylphosphine that give strong peaks across a wide range of m/z values.
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TurboIonSpray TurboIonSpray A commercial term for a version of the IonSpray source that accepts large liquid flow rates, from 2100 µL/min. Also known as turbo ion spray and turbo ionspray.
turbomolecular pump A pump used for achieving and maintaining high vacuum, once the system has been pumped down to about 0.1 Pa with a roughing pump. It consists of a series of blades mounted on a rotary shaft which rotate rapidly to draw in gases. No fluids are required to maintain the vacuum, so there is no hydrocarbon background from oils. Also known as a turbo pump.
turbulent flow chromatography
Schematic of a turbomolecular vacuum pump
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A form of HPLC in which the column is packed with large particles and a high solvent flow rate, typically around 4 ml/min, is applied. This sets up a system with internal solvent eddies around the particles. Molecules of small molecular weight diffuse faster than large ones and tend to interact more with the stationary phase in the turbulent flow. The larger molecules elute sooner and greater separation is achieved. In particular, the system is better adapted to the rapid elution of biopolymers from samples such as plasma which interfere in other LC systems.
u
U u Symbol for unified atomic mass.
Uz Parameter in the Mathieu equation representing the DC voltage applied to the analyser.
unified atomic mass unit Atomic mass (atomic weight) based upon a scale which assigns 12.00000 exactly to the isotope 12C of carbon.
unimolecular fragmentation In the relatively collision-free vacuum in which ions are analysed, any decomposition will be unimolecular in nature.
UniProt Databases A selection of databases of protein sequence and annotation data provided by the Universal Protein resource, a collaboration between the European Bioinformatics Institute, the Swiss Institute of Bioinformatics and the Protein Information Resource. The specific databases are the UniProt Knowledgebase (UniProtKB), the UniProt 161
unit resolution Reference Clusters (UniRef), and the UniProt Archive (UniParc).
unit resolution The ability to distinguish between an ion at m/z and one at m/z + 1, with a defined valley height between the peaks, across the effective mass range of an analyser. Typically the quoted resolving power for a quadrupole analyser.
unstable ion An ion that dissociates in the ion source.
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V
V V 1. The symbol for accelerating voltage, the voltage applied to the source to impart translational energy to the ions and accelerate them into the analyser. 2. Parameter in the Mathieu equation representing the amplitude of the RF signal applied to the analyser.
vn ion A fragment ion produced by high energy CID of a peptide in which the amino acid residue side chain is lost with the charge being retained on a Cterminal ion as shown in the diagram.
Vn ion
vacuum This means high vacuum rather than full vacuum and refers to the region of the mass spectrometer in which the pressure is sufficiently low to allow the majority of the ions formed to reach the detector. For most instruments, such as quadrupoles and TOFs, 10-6 Pa is the minimum pressure required but values can be higher in ion traps. 163
vacuum evaporation method vacuum evaporation method A technique for preparing a sample for MALDI analysis. A variation of the dried droplet method in which the drop of mixed matrix and sample is dried rapidly in a vacuum desiccator.
vacuum lock A device permitting the introduction of sample probes into the source while maintaining the low pressure within the source.
vacuum pump The high-vacuum pump reduces the pressure within the system from values of around 0.1 Pa that are achieved with a mechanical pump, to the operating pressures of 10-4 to 10-6 Pa. Highvacuum pumps can be oil diffusion pumps, turbomolecular pumps or cryogenic pumps.
validation In quantitative studies, the process which proves that the method is fit for its planned purpose. Validation of a specific method should be demonstrated using standards or samples that are similar to the unknown samples that will be analyzed when the method is applied.
valley The 10% and 50% valley methods are used to define the resolving power of a mass spectrometer. They refer to the degree of overlap (10 or 50%), signified by ΔM, between two adjacent peaks of equal height, and are used in the ratio M/ΔM, where M is the m/z value of the first peak.
vertical ionisation The addition or removal of an electron to a molecule so that the ion formed retains the geometry of the original molecule. In many cases, the resultant ion is formed in a vibrationally excited state.
volumetric internal standard
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An internal standard that is added to the extract of the target analyte. It need not be chemically related to the analyte but should otherwise conform to the requirements of an internal standard. It is used in conjunction with an external standard to compensate for variations in the volumes applied to the GC or LC column.
wn ion
W wn ion An ion produced by the cleavage of a peptide side chain, such as those containing isoleucine and leucine residues, with charge retention on the Cterminus. Amino acid residues with aromatic side chains do not readily undergo this fragmentation. The presence of wn ions allows the isobaric leucine and isoleucine to be differentiated.
Wn ion
Warhaftig diagram
water chiller see water cooler
AP ion sources are designed to minimise the formation of solvent cluster ions. Common clusters seen when declustering regimes are not working
A − D•+ B=C
A − B• + C = D+
P(E) A−B−C−D•+ stable ions A−B−C−D•+ produces A−D•+ in the analyzer (metastable) A−B−C−D•+ unstable produces A−D•+ in the ion source C = D+ A − D•+ 3 2 1 Parent 1 2 1ʹ 2ʹ ionization
water clusters
D•+ A B−C
log k (E)
A graphical representation of the energy distribution within an ion newly formed by EI. Three cases are distinguished: stable ions which transit the mass spectrometer unchanged, unstable ions which decompose in the ion source and metastable ions which fragment while in transit through the analyser.
A−B−C−D•+
A−B−C−D•+ produces C=D+ in the analyzer (metastable) A−B−C−D•+ unstable produces C = D+ in the ion source C = D+ dominates A−D•+
Energy
Warhaftig diagram. Reproduced from Mass Spectrometry: Principles and Applications, E. de Hoffmann and V. Stroobant, p 279, © John Wiley & Sons, Ltd
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water cooler properly include ions of a series such as H3O(H2O)n+.
water cooler A system that circulates temperature-controlled water in a closed system for cooling specific parts of an instrument.
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xn ion
X xn ion A C-terminal ion formed by fission of a peptide ion at the C-C peptide bond. See peptide sequencing
xenon An inert gas used as a collision gas in CID and as the source gas for the atom beam in FAB studies.
XIC for extracted ion chromatogram see selected ion chromatogram
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yn ion
Y yn ion A C-terminal ion formed by fission of a peptide ion at the C-N peptide bond. See peptide sequencing
ylide
An ylide ion
A neutral molecule which has positive and negative charges on adjacent atoms as shown in the diagram. The positively charged atom is usually nitrogen, phosphorus or sulphur and the negatively charged atom is generally carbon, but can be other atoms.
ynolate ion An anion which is an analogue of the enolate ion, but with a triple bond in place of the enol double bond, as shown in the diagram. An ynolate ion
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zn ion
Z zn ion A C-terminal ion formed by fission of a peptide ion at the N-C peptide bond. See peptide sequencing
zepto The prefix for 10-21. Symbol z. As in 5 zeptomoles, or 5 zmoles.
ZoomScan A commercial term to describe an advanced scan mode in an ion trap in which a narrow m/z range is acquired at higher resolution. It can be used, for example, to resolve multiple charge state distributions. The technique is not confined to instrumentation from this manufacturer.
ZSpray A commercial term to describe a two-stage LC/MS source in which the HPLC eluate follows an orthogonal path before entering the mass spectrometer. See orthogonal extraction
A commercial API Zspray ion source. Photograph by Tony Mallet
zwitterion A compound that carries positive and negative charges on different atoms, but is neutral overall, as shown in the diagram.
Zwitterion
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Suggested Reading IUPAC is the source for definitions of terms to be used in mass spectrometry. Provisional versions of the IUPAC list can be found on the worldwide web e.g. http://old.iupac.org/reports/provisional/, but the definitive text is still not published. Much further mass spectrometry information can be found in the free web site SpectroscopyNow.com.
General mass spectrometry texts: Mass Spectrometry: A Foundation course by K. Downard, RSC 2004. Mass Spectrometry: Principles and Applications, 3rd Edition by E. de Hoffmann and V. Strobant, Wiley 2007. Introduction to Mass Spectrometry: Instrumentation, Applications, and Strategies for Data Interpretation, 4th Edition by J. T. Watson and O. D. Sparkman, Wiley, 2007. Mass Spectrometry Desk Reference, 2nd Edition by O. D. Sparkman, Global View Publishing, 2006.
Gas Chromatography and mass spectrometry: GC/MS: A Practical User's Guide, 2nd Edition by M. McMaster, Wiley, 2008.
Liquid Chromatography and mass spectrometry: Liquid Chromatography – Mass Spectrometry: An Introduction by R. E. Ardrey, Wiley, 2003. Liquid Chromatography – Mass Spectrometry (Chromatographic Science), 3rd Edition by W. M. A. Niessen, CRC Press, 2006.
Quantitative analysis with mass spectrometry: Trace Quantitative Analysis by Mass Spectrometry by R. K. Boyd, C. Basic and R. A. Bethem, Wiley, 2008. Quantitative Applications of Mass Spectrometry by Pietro Traldi, Franco Magno, Irma Lavagnini and Roberta Seraglia, Wiley, 2006. Quantitative Proteomics by Mass Spectrometry (Methods in Molecular Biology) by S. Sechi, Humana Press, 2007.
ICP mass spectrometry: Practical Guide to ICP-MS (Practical Spectroscopy): A Tutorial for Beginners by R. Thomas, CRC Press, 2008. Plasma Source Mass Spectrometry: Current Trends and Future Developments (Special Publication) by D. R. Bandura and J. G. Holland, RSC, 2005.
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Biological aspects of mass spectrometry: The Expanding Role of Mass Spectrometry in Biotechnology, 2nd Edition by G. Siuzdak, MCC Press, 2006. Mass Spectrometry of Proteins and Peptides: Methods and Protocols (Methods in Molecular Biology), 2nd Edition, edited by M. S. Lipton and L. Pasa-Tolic, Springer, 2009. Introduction to Proteomics (Wiley Interscience Series on Mass Spectrometry) edited by A. Kraj and J. Silberring, Wiley, 2008. Protein Mass Spectrometry: 52 (Comprehensive Analytical Chemistry) edited by J. Whitelegge, Elsevier, 2008. Mass Spectrometry of Protein Interactions (Wiley Interscience Series on Mass Spectrometry) by K. Downard, Wiley, 2007.
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Thermo Fisher Scientific 355 River Oaks Parkway San Jose, CA 95134 USA www.thermo.com
Waters Corporation 34 Maple Street Milford, MA 01757 USA T: 1 508 478 2000 F: 1 508 872 1990 www.waters.com
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