SECOND EDITION
Edited by
Timothy D. Veenstra
Watertown, Wisconsin
John R. Yates III
Torrey Mesa, California
This Second edition first published 2019
© 2019 John Wiley & Sons, Inc.
Edition History
John Wiley & Sons, Inc. (1e 2006)
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 law. Advice on how to obtain permission to reuse material from this title is available at http://www.wiley.com/go/permissions.
The right of Timothy D. Veenstra and John R. Yates III to be identified as the Editors of the editorial material in this work has been asserted in accordance with law.
Registered Office(s)
John Wiley & Sons, Inc., 111 River Street, Hoboken, NJ 07030, USA
Editorial Office
Boschstr. 12, 69469 Weinheim, Germany
For details of our global editorial offices, customer services, and more information about Wiley products visit us at www.wiley.com.
Wiley also publishes its books in a variety of electronic formats and by print‐on‐demand. Some content that appears in standard print versions of this book may not be available in other formats.
Limit of Liability/Disclaimer of Warranty
While the publisher and authors have used their best efforts in preparing this work, they 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 merchantability or fitness for a particular purpose. No warranty may be created or extended by sales representatives, written sales materials or promotional statements for this work. The fact that an organization, website, or product is referred to in this work as a citation and/or potential source of further information does not mean that the publisher and authors endorse the information or services the organization, website, or product may provide or recommendations it may make. 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 your situation. You should consult with a specialist where appropriate. Further, readers should be aware that websites listed in this work may have changed or disappeared between when this work was written and when it is read. Neither the publisher nor authors shall be liable for any loss of profit or any other commercial damages, including but not limited to special, incidental, consequential, or other damages.
Library of Congress Cataloging‐in‐Publication Data
Names: Veenstra, Timothy Daniel, 1966– editor. | Yates III, John R., editor.
Title: Proteomics for biological discovery / edited by Timothy D. Veenstra, John R. Yates III.
Description: Second edition. | Hoboken, NJ : Wiley‐Blackwell, 2019. | Includes bibliographical references and index. |
Identifiers: LCCN 2019015129 (print) | LCCN 2019015652 (ebook) | ISBN 9781119081692 (Adobe PDF) | ISBN 9781119081722 (ePub) | ISBN 9781118279243 (hardback)
Subjects: | MESH: Proteomics | Computational Biology–methods
Classification: LCC QP551 (ebook) | LCC QP551 (print) | NLM QU 460 | DDC 612.3/98–dc23
LC record available at https://lccn.loc.gov/2019015129
Cover Design: Wiley
Cover Image: © Scala/Art Resource
A critical advance in biology was the sequencing of the human genome approximately 15 years ago. A dedicated effort to advance technology has made it feasible and cost‐effective to sequence the entire genomes of individuals with a growing use in clinical diagnosis. The growing collection of DNA sequence data has provided a powerful resource for studies involving protein biochemistry, in particular to create a better understanding of how disease mechanisms manifest from genes to proteins. Advanced methods in large‐scale protein biochemistry or proteomics have broadened the types of experiments possible.
Understanding diseases requires discovering the mechanisms by which biological processes are disrupted. These mechanisms are often manifested through proteins and their functions. Proteomic methods are now able to measure protein expression, the composition of organelles, posttranslational modifications, and protein–protein interactions to determine how proteins are changed as a function of disease. A variety of methods make these measurements possible, including mass spectrometry and protein arrays. Protein arrays allow the study of large‐scale protein expression. They also allow scanning for circulating reactive antibodies that associate with disease. These advanced methods are increasingly used for studies to identify markers for disease. Increasingly, proteomic tools are being used in the development of therapeutic treatments.
In this second edition of Proteomics for Biological Discovery, chapters describe research meeting these needs.
Mohammed and Heck describe recent advances in quantitative proteomics using mass spectrometry. Veenstra describes proteome analysis of posttranslational modifications. Delahunty and Yates describe mass spectrometry‐based methods and applications to use affinity purification mass spectrometry for characterization of protein complexes. Diamandis and Drabovich cover the process of biomarker discovery. Yates discusses the large‐scale analysis of phosphorylation in biological systems. Robinson discusses the characterization of intact protein complexes using native mass spectrometry. Borchers describes the use of protein cross‐linking to characterize protein structures and protein–protein interactions. Emili describes the use of proteomics to understand protein function. Haab discusses the use of antibodies for proteomic profiling. LaBaer describes the use of protein arrays in proteomics. Sweedler describes the use of mass spectrometry imaging. An important new area of proteomics is single cell mass cytometry which is described by Edgar Arriaga. Kuster describes how to characterize drug–protein interactions.
Timothy D. Veenstra
Department of Applied Science
Maranatha Baptist University
Watertown, WI, USA
John R. Yates III
Departments of Molecular Medicine and Neurobiology
The Scripps Research Institute, LaJolla, CA, USA
Edgar A. Arriaga
Department of Chemistry, University of Minnesota
Minneapolis, MN, USA
Marcus Bantscheff
Cellzome, Heidelberg, Germany
Christoph H. Borchers
University of Victoria – Genome British Columbia Proteomics Centre
Vancouver Island Technology Park, Victoria, BC, Canada
Claire M. Delahunty
Departments of Molecular Medicine and Neurobiology
The Scripps Research Institute, LaJolla, CA, USA
Eleftherios P. Diamandis
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
Andrei P. Drabovich
Department of Laboratory Medicine and Pathology, University of Alberta,
Edmonton, AB, Canada
Sage J.B. Dunham
Department of Chemistry and the Beckman Institute of Science and Technology
University of Illinois at Urbana–Champaign, Champaign, IL, USA
Andrew Emili
Donnelly Centre for Cellular and Biomolecular Research
University of Toronto, Toronto, ON, Canada
Fernanda Festa
Departments of Pediatrics and Biochemistry/Molecular Biology
College of Medicine, Penn State University, Hershey, PA, USA
Christian K. Frese
Biomolecular Mass Spectrometry and Proteomics
Bijvoet Center for Biomolecular Research and Utrecht Institute for
Pharmaceutical Sciences, Utrecht University, Utrecht
The Netherlands
Heather M. Grundhofer
Department of Chemistry, University of Minnesota
Minneapolis, MN, USA
Brian B. Haab
Van Andel Research Institute, Grand Rapids, MI, USA
Pierre C. Havugimana
Donnelly Centre for Cellular and Biomolecular Research, University of Toronto,
Toronto, ON, Canada
Albert J.R. Heck
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University,
Utrecht, The Netherlands
Jonathan T.S. Hopper
Department of Chemistry, Physical and Theoretical Chemistry Laboratory,
University of Oxford, Oxford, UK
Pingzhao Hu
Department of Biochemistry and Medical Genetics, University of Manitoba,
Winnipeg, MB, Canada
Michelle M. Kuhns
Department of Chemistry, University of Minnesota, Minneapolis, MN, USA
Bernhard Kuster
Cellzome, Heidelberg, Germany. Technical University Munich, F.reising,
Germany
Joshua LaBaer
Virginia G. Piper Center for Personalized Diagnostics, Biodesign Institute,
Arizona State University, Tempe, AZ, USA
Eric J. Lanni
Department of Chemistry and the Beckman Institute of Science and Technology,
University of Illinois at Urbana–Champaign, Champaign, IL, USA
Eduardo Martínez‐Morillo
Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
Shabaz Mohammed
Biomolecular Mass Spectrometry and Proteomics
Bijvoet Center for Biomolecular Research and Utrecht Institute for
Pharmaceutical Sciences, Utrecht University, Utrecht
The Netherlands
Elizabeth K. Neumann
Department of Chemistry and the Beckman Institute of Science and Technology
University of Illinois at Urbana–Champaign, Champaign, IL, USA
Ta‐Hsuan Ong
Department of Chemistry and the Beckman Institute of Science and Technology,
University of Illinois at Urbana–Champaign, Champaign, IL, USA
Evgeniy V. Petrotchenko
University of Victoria – Genome British Columbia Proteomics Centre
Vancouver Island Technology Park, Victoria, BC, Canada
Carol V. Robinson
Department of Chemistry, Physical and Theoretical Chemistry Laboratory
University of Oxford, Oxford, UK
Markus Schirle
Novartis Institutes for BioMedical Research, Inc., Cambridge, MA, USA
Jason J. Serpa
University of Victoria – Genome British Columbia Proteomics Centre
Vancouver Island Technology Park, Victoria, BC, Canada
Jonathan V. Sweedler
Department of Chemistry and the Beckman Institute of Science and Technology
University of Illinois at Urbana–Champaign, Champaign, IL, USA
Henk van den Toorn
Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for
Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences
Utrecht University, Utrecht, The Netherlands