PROTEIN SEQUENCING AND IDENTIFICATION USING TANDEM MASS SPECTROMETRY

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PROTEIN SEQUENCING AND IDENTIFICATION USING TANDEM MASS SPECTROMETRY Michael Kinter Department of Cell Biology Lerner Research Institute Cleveland Clinic Foundation

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 Singapore Toronto

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3 PROTEIN SEQUENCING AND ldentlflcatlon USING TANDEM MASS SPECTROMETRY

4 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 Forthcoming Books in the Series Chhabil Dass, Princiyles and Practice of Biological Mass Spectrometry

5 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

6 This book IS pnnted on acid-free 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) , fax (978) Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 605 Third Avenue, New York, NY , (212) , fax (212) , PERMREQ@WILEY.COM. For ordering and customer service, call 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 (cloth: alk. paper) 1. Nucleotide sequence. 2. Proteins-Identification. 3. Mass spectrometry. I. Sherman, Nicholas. 11. Title. QP55l.K ~ Printed in the United States of America

7 To Caroline, Lauren, and Courtney Karen and Abby

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9 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 The Edman Reaction Incorporation of the Edman Degradation Reaction into Automated Protein Sequenators Edman Degradation in Proteomic Research 2.3. Tandem Mass Spectrometry 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 vii

10 Viii CONTENTS 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 Chapter 3. Fundamental Mass Spectrometry An Overview of the Instrumentation Ionization Methods Electrospray Ionization Nanospray and Microspray Ionization Matrix-Assisted Laser Desorption/ Ionization Mass Analyzers Fundamental Parameters of Mass Analysis Quadrupole Mass Filters (3.20) Ion Trap Mass Analyzers ( ) Time-of-Flight Mass Analyzers (3.5) Tandem Mass Spectrometry Collisionally Induced Dissociation Tandem Mass Spectrometers Types of Tandem Mass Spectrometry Data Systems Summary References Experiments Chapter 4. Collisionally Induced Dissociation of Protonated Peptide Ions and the Interpretation of Product Ion Spectra 4.1. Introduction 4.2. Peptide Fragmentation Chemistry Collisionally Induced Dissociation of Peptide Ions Formed by Electrospray Ionization Fragmentation of Protonated Peptide Ions Formed by Matrix-Assisted Laser Desorption/Ionization Interpretation of the Product Ion Spectra of Tryptic Peptides

11 CONTENTS Tabulated Values Used in the Interpretation A Strategy for the Interpretation of Product Ion Spectra of Tryptic Peptides Sample Interpretation Problem Number One Sample Interpretation Problem Number Two A Summary of Interpretation Problems One and Two Examples of More Difficult Product Ion Spectra That Cannot Be Completely Interpreted Interpretation of Product Ion Spectra from Triply Charged Ions 4.4. Summary 4.5. References ix Chapter 5. Basic Polyacrylamide Gel Electrophoresis 5.1. Introduction 5.2. The Principles of Gel Electrophoresis Protein Movement and Separation Protein Detection 5.3. The Basic Steps in a Polyacrylamide Gel Electrophoresis Experiment SDS-PAGE Gels for Protein Molecular Weight Measurements Isoelectric Focusing Gels Protein Detection Data Analysis The Protein Sample Presented for Digestion and Amino Acid Sequence Analysis Example Protocols for 2D Electrophoresis with Immobilized ph-gradient Gels 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

12 X CONTENTS 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 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 Protein Band Selection The In-Gel Digestion Protocol 6.5. An In-Solution Digestion Protocol The In-Solution Digestion Protocol 6.6. Summary 6.7. References 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 Capillary Column Liquid Chromatography The Acquisition and Presentation of Mass Spectra Chromatogram Reconstruction The Determination of Peptide Molecular Weights The Characterization of Peptide Structure Automated Acquisition of Both Mass Spectra and Product Ion Spectra

13 7.3. CONTENTS Benchmark Performance of a Capillary Column Liquid Chromatography- Electrospray Ionization-Tandem Mass Spectrometry Experiment Improving Sensitivity Through the Use of Microspray Ionization 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 The Acquisition and Presentation of Mass Spectra The Determination of Peptide Molecular Weights The Characterization of Peptide Structure Automated Data Acquisition Benchmark Performance of a Delayed Extraction-Reflectron Time-of-Flight Mass Spectrometry Experiment A Protocol for Sample Desalting by Solid Summary 7.5. Reference Phase Extraction Prior to Analysis xi Chapter 8. Protein Identification by Database Searching Introduction The Sequence Databases The Protein Sequence Databases The Genomic and Expressed Sequence Tag Databases Database Search Programs for Use with Mass Spectrometric Protein Sequencing Data Database Searching with Amino Acid Sequences Database Searching with Peptide Molecular Weights Database Searching with Uninterpreted Product Ion Spectra Reporting the Results of a Protein Identification Summary References

14 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 Fragmentation of Product Ions Synthetic Peptides Peptide Derivatization Edman Degradation 9.4. Using Mass Spectrometric Data to Verify the Results of Cloning Experiments 9.5. Summary 9.6. References Chapter 10. The Characterization of Post-Translationally Modified Proteins Using Tandem Mass Spectrometry Introduction An Overview of the Methods Identifying Modified Peptides Ions by Searching for Calculated Molecular Weights Identifying Modified Peptides by Observation of Specific Fragmentation Reactions Isolating Modified Peptides by Affinity Chromatography Prior to Tandem Mass Spectrometric Characterization Examples of Experiments Characterizing Specific Post-Translational Modifications Phosphorylation Xenobiotic Modification Carbohydrate Modification Summary References Index 295

15 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

TRANSPORT PHENOMENA AND UNIT OPERATIONS

TRANSPORT PHENOMENA AND UNIT OPERATIONS TRANSPORT PHENOMENA AND UNIT OPERATIONS A COMBINED APPROACH Richard G. Griskey A JOHN WILEY & SONS, INC., PUBLICATION This book is printed on acid-free paper Copyright