PROTEIN SEQUENCING AND IDENTIFICATION USING TANDEM MASS SPECTROMETRY

PROTEIN SEQUENCING AND IDENTIFICATION USING TANDEM MASS SPECTROMETRY Michael Kinter Department of Cell Biology Lerner Research Institute Cleveland Clinic Foundation Nicholas E. Sherman Department of Microbiology University of Virginia WILEY- INTERSCI ENCE A JOHN WILEY & SONS, INC., PUBLICATION New York Chichester Weinheim Singapore Toronto

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PROTEIN SEQUENCING AND ldentlflcatlon USING TANDEM MASS SPECTROMETRY

Wiley-Interscience Series on Mass Spectrometry Series Editors Dominic M. Desiderio Departments of Neurology and Biochemistry University of Tennessee Health Science Center Nico M. M. Nibbering University of Amsterdam The aim of the series is to provide books written by experts in the various disciplines of mass spectrometry, including but not limited to basic and fimdamental research, instrument and methodological developments, and applied research. Books in the Series Michael Kinter, Protein Sequencing and IdentiJication Using Tandem Mass Spectrometry 0-47 1-32249-07 Forthcoming Books in the Series Chhabil Dass, Princiyles and Practice of Biological Mass Spectrometry 0-47 1-33053-1

PROTEIN SEQUENCING AND IDENTIFICATION USING TANDEM MASS SPECTROMETRY Michael Kinter Department of Cell Biology Lerner Research Institute Cleveland Clinic Foundation Nicholas E. Sherman Department of Microbiology University of Virginia WILEY- INTERSCI ENCE A JOHN WILEY & SONS, INC., PUBLICATION New York Chichester Weinheim Brisbane Singapore Toronto

This book IS pnnted on acid-free paper @ Copynght 6, 2000 by John Wiley & Sons, Inc All nghts reserved Published simultaneously in Canada 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, scanning or otherwise, except as permitted under Sections 107 or 108 of the 1976 United States Copyright Act, without either the prior written permission of the Publisher, or authorization through payment of the appropriate per-copy fee to the Copyright Clearance Center, 222 Rosewood Drive, Danvers, MA 01923, (978) 750-8400, fax (978) 750-4744. Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY 10158-0012, (212) 850-601 1, fax (212) 850-6008, E-Mail: PERMREQ@WILEY.COM. For ordering and customer service, call 1-800-CALL-WILEY. Library of Congress Cataloging-in-Publication Data: Kinter, Michael. Protein sequencing and identification using tandem mass spectrometq / Michael Kinter, Nicholas E. Sherman. p. cm. Includes bibliographical references and index. ISBN 0-471-32249-0 (cloth: alk. paper) 1. Nucleotide sequence. 2. Proteins-Identification. 3. Mass spectrometry. I. Sherman, Nicholas. 11. Title. QP55l.K495 2000 572.8 54~21 00-038204 Printed in the United States of America. 109 8 7 6 5

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CONTENTS Series Preface Preface xiii xv Chapter 1. Chapter 2. An Introduction to Protein Sequencing Using Tandem Mass Spectrometry 1.1. Introduction 1.2. References The Primary Structure of Proteins and a Historical Overview of Protein Sequencing 2.1. Protein and Peptide Structure 2.2. Edman Degradation 2.2.1. The Edman Reaction 2.2.2. Incorporation of the Edman Degradation Reaction into Automated Protein Sequenators 2.2.3. Edman Degradation in Proteomic Research 2.3. Tandem Mass Spectrometry 2.3.1. 2.3.2. 2.3.3. A Brief History of the Application of Mass Spectrometry to Protein Sequencing Sequence Analysis of Peptides Using Electron Ionization Mass Spectrometry The Utilization of Fast Atom Bombardment with Tandem Mass Spectrometry to Sequence Peptides 6 6 10 10 11 14 15 15 16 17 vii

Viii CONTENTS 2.3.4. Internal Sequence Analysis of Proteins Using Electrospray Ionization-Tandem Mass Spectrometry and Matrix-Assisted Laser Desorption/Ionization-Time-of- Flight Mass Spectrometry 2.4. Summary 2.5. References 19 22 23 Chapter 3. Fundamental Mass Spectrometry 3.1. 3.2. 3.3. 3.4. 3.5. 3.6. 3.7. An Overview of the Instrumentation Ionization Methods 3.2.1. Electrospray Ionization 3.2.2. Nanospray and Microspray Ionization 3.2.3. Matrix-Assisted Laser Desorption/ Ionization Mass Analyzers 3.3.1. Fundamental Parameters of Mass Analysis 3.3.2. Quadrupole Mass Filters (3.20) 3.3.3. Ion Trap Mass Analyzers (3.21-3.23) 3.3.4. Time-of-Flight Mass Analyzers (3.5) Tandem Mass Spectrometry 3.4.1. Collisionally Induced Dissociation 3.4.2. Tandem Mass Spectrometers 3.4.3. Types of Tandem Mass Spectrometry Data Systems Summary References Experiments 29 29 31 32 36 37 39 40 43 45 48 52 52 53 57 59 61 61 Chapter 4. Collisionally Induced Dissociation of Protonated Peptide Ions and the Interpretation of Product Ion Spectra 4.1. Introduction 4.2. Peptide Fragmentation Chemistry 4.2.1. Collisionally Induced Dissociation of Peptide Ions Formed by Electrospray 4.3. 4.2.2. Ionization Fragmentation of Protonated Peptide Ions Formed by Matrix-Assisted Laser Desorption/Ionization Interpretation of the Product Ion Spectra of Tryptic Peptides 64 64 65 66 79 81

CONTENTS 4.3.1. Tabulated Values Used in the Interpretation 4.3.2. A Strategy for the Interpretation of Product Ion Spectra of Tryptic Peptides 4.3.3. Sample Interpretation Problem Number One 4.3.4. Sample Interpretation Problem Number Two 4.3.5. A Summary of Interpretation Problems One and Two 4.3.6. Examples of More Difficult Product Ion Spectra That Cannot Be Completely Interpreted 4.3.7. Interpretation of Product Ion Spectra from Triply Charged Ions 4.4. Summary 4.5. References ix 81 86 89 94 99 100 110 114 115 Chapter 5. Basic Polyacrylamide Gel Electrophoresis 5.1. Introduction 5.2. The Principles of Gel Electrophoresis 5.2.1. Protein Movement and Separation 5.2.2. Protein Detection 5.3. The Basic Steps in a Polyacrylamide Gel Electrophoresis Experiment 5.3.1. SDS-PAGE Gels for Protein Molecular 5.4. 5.5. Weight Measurements 5.3.2. Isoelectric Focusing Gels 5.3.3. Protein Detection 5.3.4. Data Analysis The Protein Sample Presented for Digestion and Amino Acid Sequence Analysis Example Protocols for 2D Electrophoresis with Immobilized ph-gradient Gels 5.5.1. 5.5.2. 5.5.3. A Protocol for the Preparation of a Protein Homogenate, from Cultured Mammalian Cells, for Isoelectric Focusing in an Immobilized ph-gradient Gel A Protocol for the Passive Rehydration of Immobilized ph-gradient Gels A Protocol for the Active Rehydration of Immobilized ph-gradient Gels 117 117 118 118 123 124 125 128 131 133 133 135 135 138 139

X CONTENTS 5.5.4. 5.5.5. 5.5.6. 5.5.7. 5.6. Summary 5.7. References A Protocol for the Equilibration, with Reduction and Alkylation, of an Immobilized ph-gradient Gel for Molecular Weight Analysis by SDS-PAGE A Protocol for Staining Polyacrylamide Gels with Coomassie Blue A Protocol for Staining Polyacrylamide Gels with Colloidal Coomassie Blue A Protocol for Silver-Staining Polyacrylamide Gels 140 141 143 144 145 146 Chapter 6. The Preparation of Protein Digests for Mass Spectrometric Sequencing Experiments 6.1. Introduction 6.2. Protease Selection 6.3. The Effects of Contamination 6.4. An In-Gel Digestion Protocol 6.4.1. Protein Band Selection 6.4.2. The In-Gel Digestion Protocol 6.5. An In-Solution Digestion Protocol 6.5.1. The In-Solution Digestion Protocol 6.6. Summary 6.7. References 147 147 148 150 152 153 153 160 161 163 164 Chapter 7. Mass Spectrometric Analysis of Tryptic Digests 7.1. Introduction 7.2. Mass Spectrometric Analysis of Tryptic Digests Using Capillary Column Liquid Chromatography- Electrospray Ionization-Tandem Mass Spectrometry 7.2.1. Capillary Column Liquid Chromatography 7.2.2. The Acquisition and Presentation of Mass Spectra 7.2.3. Chromatogram Reconstruction 7.2.4. The Determination of Peptide Molecular Weights 7.2.5. The Characterization of Peptide Structure 7.2.6. Automated Acquisition of Both Mass Spectra and Product Ion Spectra 166 166 168 168 172 174 176 178 179

7.3. CONTENTS 7.2.7. Benchmark Performance of a Capillary Column Liquid Chromatography- Electrospray Ionization-Tandem Mass Spectrometry Experiment 7.2.8. Improving Sensitivity Through the Use of Microspray Ionization 7.2.9. A Protocol for Packing a Capillary Liquid Chromatography Column Mass Spectrometric Analysis of Tryptic Digests by Matrix-Assisted Laser Desorption/Ionization-Timeof-Flight Mass Spectrometry 7.3.1. The Acquisition and Presentation of Mass Spectra 7.3.2. The Determination of Peptide Molecular Weights 7.3.3. The Characterization of Peptide Structure 7.3.4. Automated Data Acquisition 7.3.5. Benchmark Performance of a Delayed Extraction-Reflectron Time-of-Flight Mass Spectrometry Experiment 7.3.6. A Protocol for Sample Desalting by Solid- 7.4. Summary 7.5. Reference Phase Extraction Prior to Analysis xi 182 190 191 194 195 197 199 200 20 1 203 206 206 Chapter 8. Protein Identification by Database Searching 207 8.1. 8.2. 8.3. 8.4. 8.5. 8.6. Introduction The Sequence Databases 8.2.1. The Protein Sequence Databases 8.2.2. The Genomic and Expressed Sequence Tag Databases Database Search Programs for Use with Mass Spectrometric Protein Sequencing Data 8.3.1. Database Searching with Amino Acid Sequences 8.3.2. Database Searching with Peptide Molecular Weights 8.3.3. Database Searching with Uninterpreted Product Ion Spectra Reporting the Results of a Protein Identification Summary References 207 208 208 21 1 212 212 219 226 234 235 236

xii CONTENTS Chapter 9. Sequence Analysis of Novel Proteins 9.1. Introduction 9.2. The Role of Confirmation in the Interpretation Process 9.3. Strategies to Enhance and Confirm the Interpretation of Product Spectra 9.3.1. Fragmentation of Product Ions 9.3.2. Synthetic Peptides 9.3.3. Peptide Derivatization 9.3.4. Edman Degradation 9.4. Using Mass Spectrometric Data to Verify the Results of Cloning Experiments 9.5. Summary 9.6. References 238 23 8 24 1 24 1 243 25 1 254 259 265 267 267 Chapter 10. The Characterization of Post-Translationally Modified Proteins Using Tandem Mass Spectrometry 10.1. Introduction 10.2. An Overview of the Methods 10.2.1. Identifying Modified Peptides Ions by Searching for Calculated Molecular Weights 10.2.2. Identifying Modified Peptides by Observation of Specific Fragmentation Reactions 10.2.3. Isolating Modified Peptides by Affinity Chromatography Prior to Tandem Mass Spectrometric Characterization 10.3. Examples of Experiments Characterizing Specific Post-Translational Modifications 10.3.1. Phosphorylation 10.3.2. Xenobiotic Modification 10.3.3. Carbohydrate Modification 10.4. Summary 10.5. References 269 269 272 273 276 277 279 280 285 287 290 290 Index 295

SERIES PREFACE The aim of this series is to provide a series of volumes written by experts in various disciplines of mass spectrometry, including basic and fimdamental research, instrument and methodological developments, and applied research. The books in this series will be of use to researchers who use mass spectrometry and wish to focus on one particular area, to teachers in the classroom, and to newcomers to the field of mass spectrometry. Each discipline listed above is developing and expanding at a rapid rate, and this book series will provide an effective means to collect all of the pertinent information in each area. Finally, the sum total of the research collected within this book series will be of interest to researchers in related areas such as chemistry, physics, biology, medicine, nutrition, and other areas. xiii