See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/261097310 The Mass Spectrometry Primer Book in Lc Gc North America · March 2009 CITATIONS READS 6 1,400 1 author: Michael Balogh Waters Corporation 14 PUBLICATIONS 217 CITATIONS SEE PROFILE All content following this page was uploaded by Michael Balogh on 26 March 2014. The user has requested enhancement of the downloaded file. The Mass Spectrometry Primer Michael P. Balogh Copyright © 2009 Waters Corporation All rights reserved. No part of this book may be reproduced or transmitted in any form by any means, electronic or mechanical, including photocopying, recording, or by any other information storage and retrieval system, without permission from the Publisher. Waters Corporation 34 Maple Street Milford, MA 01757 Library of Congress Control Number: 2009921480 Printed in the USA © Waters Corporation. Waters, The Science of What’s Possible, ACQUITY UPLC, SYNAPT, High Definition Mass Spectrometry, TriWave, UPLC, AutoSpec are trademarks of Waters Corporation. Google is a trademark of Google Inc. LCGC is a registered trademark of Advanstar Communications. Sigma Aldrich is a registered trademark of Sigma-Aldrich Co. PEEK is a trademark of Victrex plc. February 2009 715001940 VW-FP Preface Information in any form committed to public view must be of high scholarly order. It is also true that once words have been printed the value of the meaning they impart decreases as new understanding takes shape. This primer covers a wide range of topics related to the most wide spread of modern mass spectrom- etry practices and answers some frequently asked questions about the use and capabilities of mass spectrometers. Links are also provided to articles for more in-depth reading. The first section examines who uses mass spectrometers, followed by how compounds are ionized in the source to be analyzed by mass spectrometers. A description of the various types of mass spectrometers is followed by a discussion of the important topics of mass accuracy and resolution—or how well we can tell differences between closely related compounds. Chemistry, sample prep, and data handling are considered, as well as the definition of some terms commonly used in the most prevalent forms of MS practice today. Primers in different forms can be found from a variety of authors and many of them are referenced for further reading in this one. The electronic version of this primer resides on the Waters website displaying a sidebar offering readers the opportunity to comment (see www.waters.com/primers). So what makes this one different is its inherent continually self-validating existence based on its use as it resides on the web. Succeeding versions of both the electronic version and later editions of the printed version will reflect that. Michael P. Balogh Principal Scientist, MS Technology Development Waters Corporation [ Table of Contents ] Table of Contents Who Uses Mass Spectrometry? ........................................................................................ 7 What are Mass Spectrometer? How Do They Work? .......................................................... 9 How Large a Molecule can I Analyze? ...................................................................................12 Isotope and Elemental Mass Spectrometry ...........................................................................12 Common Ionization Methods? ........................................................................................13 Electron Ionization (EI) ...........................................................................................................13 Chemical Ionization (CI) .........................................................................................................13 Negative Ion Chemical Ionization (NCI) .................................................................................15 Common Separation and Sample Delivery Methods ........................................................15 Gas Chromatography (GC) ......................................................................................................15 Liquid Chromatography (LC) ..................................................................................................16 Atmospheric Ionization Methods ...................................................................................17 Electrospray Ionization (ESI) ..................................................................................................17 Atmospheric-Pressure Chemical Ionization (APCI) ...............................................................19 Bio-Molecular Ionization Methods .........................................................................................20 Alternative Ionization Means .................................................................................................21 Atmospheric Pressure Photoionization (APPI) ............................................................21 Matrix-Assisted Laser Desorption (MALDI) .................................................................21 Fast Atom Bombardment (FAB) ....................................................................................21 Desorption .....................................................................................................................22 A Brief History of Mass Spectrometry ............................................................................23 What Types of Instruments are in Use? ..........................................................................24 The Analyzer: The Heart of a Mass Spectrometer ...........................................................25 Quadrupoles and Magnetic Sectors .......................................................................................25 Fragmentation.........................................................................................................................27 Ion Traps and Other Non-Scanning Instruments ...................................................................30 Hybrids ..................................................................................................................................34 [ Table of Contents ] Data Handling ...............................................................................................................39 Data Output, Storage, and Retrieval .............................................................................................39 Mass Accuracy and Resolution .......................................................................................40 High Mass Accuracy and Low Resolution .....................................................................................41 How Much Accuracy Do We Need, or Can Realistically Achieve, and What are the Compromises? ............................................................................................................42 Comparing Precision from Instrument to Instrument: Millimass Units (mmu), Measurement Error (ppm), and Resolution ............................................................................44 Terminology ............................................................................................................................48 Interpreting Mass-Spectrometer Output .........................................................................50 Isotope Characteristics ...........................................................................................................50 Even and Odd Electron Ions ...................................................................................................51 Characterizing Spectra Produced by Desorption and Soft Ionization ..................................52 Quantitation and Calibration .........................................................................................55 Calibration...............................................................................................................................56 Lock Mass ................................................................................................................................57 Solvents and Caveats for LCMS ......................................................................................58 Ion Suppression.......................................................................................................................60 Column Chemistries ................................................................................................................60 Ultra-High Pressure LC vs. Traditional HPLC .........................................................................61 Acknowledgements .......................................................................................................64 Glossary ......................................................................................................................65 [ List of Figures ] List of Figures & Tables Figure 1: Choosing the appropriate mass spectrometer .................................................................................7 Figure 2: Reading the mass spectrometer output .........................................................................................10 Figure 3: Choosing the mass spectrometer with enough resolution for the analysis .................................11 Figure 4: Schematic of an ESI source .............................................................................................................17 Figure 5: After formation the ions are “dragged” through