PROTEOMICS TODAY Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology
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1 PROTEOMICS TODAY Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology MAHMOUD HAMDAN GlaxoSmithKline PIER GIORGIO RIGHETTI University of Verona, Italy A JOHN WILEY & SONS, INC., PUBLICATION
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3 PROTEOMICS TODAY
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5 PROTEOMICS TODAY Protein Assessment and Biomarkers Using Mass Spectrometry, 2D Electrophoresis, and Microarray Technology MAHMOUD HAMDAN GlaxoSmithKline PIER GIORGIO RIGHETTI University of Verona, Italy A JOHN WILEY & SONS, INC., PUBLICATION
6 Copyright C 2005 by John Wiley & Sons, Inc. All rights reserved. Published by John Wiley & Sons, Inc., Hoboken, New Jersey. 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 Section 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, Inc., 222 Rosewood Drive Danvers, MA 01923, , fax , or on the web at Requests to the Publisher for permission should be addressed to the Permissions Department, John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, (201) , fax (201) Limit of Liability/Disclaimer of Warranty: While the publisher and author have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives or written sales materials. The advice and strategies contained herein may not be suitable for your situation. You should consult with a professional where appropriate. Neither the publisher nor author shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages. For general information on our other products and services please contact our Customer Care Department within the U.S. at , outside the U.S. at or fax Wiley also publishes its books in a variety of electronic formats. Some content that appears in print, however, may not be available in electronic format. Library of Congress Cataloging-in-Publication Data Proteomics today: Protein assessment and biomarkers using mass spectrometry, 2D electrophoresis, and microarray technology / Mahmoud Hamdan, Pier Giorgio Righetti. p. cm. Includes bibliographical references and index. ISBN (cloth) 1. Proteins Spectra. 2. Mass spectrometry. 3. Proteomics. I. Hamdan, Mahmoud, 1947-II. Righetti, P. G. QP551.M dc Printed in the United States of America
7 To Fatima, Giovanna, Mohammed, Jamilah To my nephews Mohsin, Hamdan, Mahmoud and Suad M.H.
8
9 CONTENTS PREFACE TO PART I ACKNOWLEDGMENT XV XVII I INTRODUCTION TO PART I 1 1 INSTRUMENTATION AND DEVELOPMENTS Introduction / Ionization Techniques for Macromolecules / Cf Plasma Desorption Ionization / Fast Atom/Ion Bombardment / Type of Fragment Ions and Nomenclature / Examples on Analytical Solutions Based on FAB MS / Detection of Abnormalities in Hemoglobin / Glycoprotein Structure Determination / Early Scanning Functions on Sector Machines / Electrospray Ionization / Matrix-Assisted Laser Desorption Ionization / MALDI at High Pressure / 21 vii
10 viii CONTENTS Desorption Ionization on Silicon (DIOS) / Delayed Extraction / Ion Detection / Microchannel Plates (MCPs) / Cryogenic Detectors / Superconducting Tunnel Junction / Thermal Detectors / Types of Analyzers / Quadrupole Mass Filter / Three-Dimensional Quadrupole Ion Trap / Linear Ion Trap / Time of Flight / Fourier Transform Ion Cyclotron Resonance / Hybrid Analyzers / Quadrupole Time of Flight / Ion Mobility TOF / Linear Ion Trap FT ICR / Ion Trap TOF / Tandem Mass Spectrometry / Postsource Decay / MS MS Measurements / Collisional Activation / Current MS Instrumentation in Proteome Analyses / MALDI TOF / MALDI TOF TOF / FT ICR MS / ION Mobility MS / Current MS-Based Proteomics / Delivering Peptides to Ion Source / Peptide Sequencing and Database Searching / Peptide Mass Fingerprinting / Searching with MS MS Data / Databases for MS Data Search / Recent Achievements and Future Challenges / Current Applications / Signal Transduction Pathways / Concluding Remarks / 61 References / 63
11 CONTENTS ix 2 PROTEOMICS IN CANCER RESEARCH Introduction / Two-Dimensional Gel Electrophoresis / Surface-Enhanced Laser Desorption Ionization / Protein Microarrays / Getting More Than Just Simple Change in Protein Expression / Laser Capture Microdissection / Pancreatic Ductal Adenocarcinoma / Analyses Based on Chip Technology / SELDI Analysis of Pancreatic Ductal Adenocarcinoma / Protein Profiling Following Treatment with DNA Methylation/Histone Deacetylation Inhibitors / Proteomic Profiling of PDAC Following Treatment with Trichostatin A / Proteomic Profiling of PDAC Following Treatment with 5 -aza-2 -deoxycytidine / Proteomic Analysis of Human Breast Carcinoma / Two-DE Analysis in Breast Cancer / Proteomic Profiling of Breast Cancer Cell Membranes / Proteomic Analysis on Selected Tissue Samples / Proteomic Profiling of Chemoresistant Cancer Cells / Protein Alterations in Pancreas Carcinoma Cells Exposed to Anticancer Drug / Proteomic Profiling of Cervix Squamous Cell Carcinoma Treated with Cisplatin / Signal Pathway Profiling of Prostate Cancer / Emerging Role of Functional and Activity-Based Proteomics in Disease Understanding / Activity-Based Protein Profiling / Probing Protein Functions Using Chromophore-Assisted Laser Inactivation / Role of Protein Tyrosine Kinases / Concluding Remarks and Future Prospects / 109 References / CURRENT STRATEGIES FOR PROTEIN QUANTIFICATION Introduction / Strategies Based on Labeling a Specific Amino Acid Residue / Isotope-Coded Affinity Tags / 128
12 x CONTENTS Two-Dimensional Gel Electrophoresis/MALDI TOF MS / Labeling Lysine Residues / Labeling Tryptophan Residues / Methionine-Containing Peptides / Global Internal Standard Technology / Acylation / Esterification / Incorporation of Heavy Isotopes / Differential In-Gel Electrophoresis / Quantification of Modified Proteins / Detection and Quantification of Phosphorylated Proteins / Detection and Quantification of Glycosylated Proteins / Ubiquitination / Comments and Considerations / Method of Separation / Detection / Other Approaches / Imaging Mass Spectrometry / Microarrays in Protein Quantification / Protein Recognition Molecules / Surface Chemistry / Some Applications / Emerging Role of Microfluidic Devices / Sample Preparation and Sample Delivery / Concluding Remarks / 174 References / 177 II PROTEOMICS TODAY: SEPARATION SCIENCE AT WORK CONVENTIONAL ISOELECTRIC FOCUSING IN GEL MATRICES AND CAPILLARIES AND IMMOBILIZED ph GRADIENTS Introduction / Brief Historical Survey / Conventional Isoelectric Focusing in Amphoteric Buffers / General Considerations / Basic Method / 190
13 CONTENTS xi Applications and Limitations / Specific Advantages / Carrier Ampholytes / Equipment / Electrophoretic Equipment / Polymerization Cassette / Polyacrylamide Gel Matrix / Reagents / Gel Formulations / Choice of Carrier Ampholytes / Gel Preparation and Electrophoresis / Assembling Gel Mold / Filling Mold / Gel Polymerization / Sample Loading and Electrophoresis / General Protein Staining / Micellar Coomassie Blue G-250 / Coomassie Blue R-250/CuSO 4 / Coomassie Blue R-250/Sulfosalicylic Acid / Coomassie Blue G-250/Urea/Perchloric Acid / Silver Stain / Specific Protein Detection Methods / Quantitation of Focused Bands / Troubleshooting / Waviness of Bands Near Anode / Burning along Cathodic Strip / ph Gradients Different from Expected / Sample Precipitation at Application Point / Some Typical Applications of IEF / Examples of Some Fractionations / Artifacts or Not? / Immobilized ph Gradients / General Considerations / Problems of Conventional IEF / Immobiline Matrix / Narrow and Ultranarrow ph Gradients / Extended ph Gradients: General Rules for Their Generation and Optimization / 230
14 xii CONTENTS Nonlinear, Extended ph Gradients / Extremely Alkaline ph Gradients / IPG Methodology / Casting an Immobiline Gel / Reswelling Dry Immobiline Gels / Electrophoresis / Staining and ph Measurements / Storage of Immobiline Chemicals / Mixed-Bed CA IPG Gels / Troubleshooting / Some Analytical Results with IPGs / Capillary Isoelectric Focusing / General Considerations / cief Methodology / Increasing Resolution by Altering Slope of ph Gradient / On Problem of Protein Solubility at Their pi / Assessment of ph Gradients and pi Values in cief / Separation of Peptides and Proteins by CZE in Isoelectric Buffers / General Properties of Amphoteric, Isoelectric Buffers / Troubleshooting for CZE in Isoelectric Buffers / Novel EOF Modulators / Conclusions / 260 References / SODIUM DODECYL SULFATE POLYACRYLAMIDE GEL ELECTROPHORESIS Introduction / SDS Protein Complexes: a Refinement of the Model / Theoretical Background of M r Measurement by SDS PAGE / Methodology / Purity and Detection of SDS / Molecular Mass Markers / Prelabeling with Dyes or Fluorescent Markers / Postelectrophoretic Detection / Nondiamine, Silver Nitrate Stain / Colloidal Staining / Hot Coomassie Staining / 288
15 CONTENTS xiii Turbidimetric Protein Detection (Negative Stain) / Negative Metal Stains / Fluorescent Detection / Possible Sources of Artifactual Protein Modification / On Use and Properties of Surfactants / The Use of Surfactants Other Than SDS / Acid-Labile Surfactants / Anomalous Behavior / Gel Casting and Buffer Systems / Sample Pretreatment / Standard Method Using Continuous Buffers / Composition of Gels and Buffers / Use of Discontinuous Buffers / Method of Neville / Method of Laemmli / Porosity Gradient Gels / Peptide Mapping by SDS PAGE / SDS PAGE in Photopolymerized Gels / Blue Native PAGE and Other Native PAGE Protocols / Blotting Procedures / Capillary and Electrophoretic Transfer / Detection Systems after Blotting / Conclusions / 331 References / TWO-DIMENSIONAL MAPS Introduction / Early Days and Evolution of 2D PAGE / A Glimpse at Modern Times / Some Basic Methodology Pertaining to 2D PAGE / Methods of Cell Disruption / Proteolytic Attack during Cell Disruption / Precipitation Procedures / Removal of Interfering Substances / Solubilization Cocktail / Sample Application / Sequential Sample Extraction / True Artifacts and Fata Morganas / 371
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