M e t h o d s in Molecular Biology

Transcription

1 M e t h o d s in Molecular Biology Series Editor John M. Walker School of Life and Medical Sciences University of Hertfordshire Hatfield, Hertfordshire, AL10 9AB, UK For further volumes:

2 Proteome Bioinformatics Edited by Shivakumar Keerthikumar and Suresh Mathivanan Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia

3 Editors Shivakumar Keerthikumar Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne, VIC, Australia Suresh Mathivanan Department of Biochemistry and Genetics La Trobe Institute for Molecular Science La Trobe University Melbourne, VIC, Australia ISSN ISSN (electronic) Methods in Molecular Biology ISBN ISBN (ebook) DOI / Library of Congress Control Number: Springer Science+Business Media LLC 2017 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. Printed on acid-free paper This Humana Press imprint is published by Springer Nature The registered company is Springer Science+Business Media LLC The registered company address is: 233 Spring Street, New York, NY 10013, U.S.A.

4 Preface Recently, mass spectrometry (MS) instrumentation and computational tools have witnessed significant advancements. Thus, MS-based proteomics continuously improved the way proteins are identified and functionally characterized. This book covers the most recent proteomics techniques, databases, bioinformatics tools, and computational approaches that are used for the identification and functional annotation of proteins and their structure. The most recent proteomic resources widely used in the biomedical scientific community for storage and dissemination of data are discussed. In addition, specific MS/MS spectrum similarity scoring functions and their application in the field of proteomics, statistical evaluation of labeled comparative proteomics using permutation testing, and methods of phylogenetic analysis using MS data are also described in detail. This edition includes recent cutting-edge technologies and methods for protein identification and quantification using tandem MS techniques. The reader gets the details of both experimental and computational methods and strategies in the identifications and functional annotation of proteins. Readers are expected to have basic bioinformatics and computational skills for a clear understanding of this book. We hope the scope of this book is useful for researchers who are beginners as well as advanced in the field of proteomics. We are extremely grateful to our colleagues who contributed high-quality chapters to this book. We thank the Springer publishers for their support and are grateful to Professor Emeritus John Walker. Melbourne, VIC, Australia Shivakumar Keerthikumar Suresh Mathivanan v

5 Contents Preface.... v Contributors... ix 1 An Introduction to Proteome Bioinformatics... 1 Shivakumar Keerthikumar 2 Proteomic Data Storage and Sharing Shivakumar Keerthikumar and Suresh Mathivanan 3 Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data Dhirendra Kumar, Amit Kumar Yadav, and Debasis Dash 4 Label-Based and Label-Free Strategies for Protein Quantitation Sushma Anand, Monisha Samuel, Ching-Seng Ang, Shivakumar Keerthikumar, and Suresh Mathivanan 5 TMT One-Stop Shop: From Reliable Sample Preparation to Computational Analysis Platform Mehdi Mirzaei, Dana Pascovici, Jemma X. Wu, Joel Chick, Yunqi Wu, Brett Cooke, Paul Haynes, and Mark P. Molloy 6 Unassigned MS/MS Spectra: Who Am I? Mohashin Pathan, Monisha Samuel, Shivakumar Keerthikumar, and Suresh Mathivanan 7 Methods to Calculate Spectrum Similarity Şule Yilmaz, Elien Vandermarliere, and Lennart Martens 8 Proteotypic Peptides and Their Applications Shivakumar Keerthikumar and Suresh Mathivanan 9 Statistical Evaluation of Labeled Comparative Profiling Proteomics Experiments Using Permutation Test Hien D. Nguyen, Geoffrey J. McLachlan, and Michelle M. Hill 10 De Novo Peptide Sequencing: Deep Mining of High- Resolution Mass Spectrometry Data Mohammad Tawhidul Islam, Abidali Mohamedali, Criselda Santan Fernandes, Mark S. Baker, and Shoba Ranganathan 11 Phylogenetic Analysis Using Protein Mass Spectrometry Shiyong Ma, Kevin M. Downard, and Jason W. H. Wong 12 Bioinformatics Methods to Deduce Biological Interpretation from Proteomics Data Krishna Patel, Manika Singh, and Harsha Gowda 13 A Systematic Bioinformatics Approach to Identify High Quality Mass Spectrometry Data and Functionally Annotate Proteins and Proteomes Mohammad Tawhidul Islam, Abidali Mohamedali, Seong Beom Ahn, Ishmam Nawar, Mark S. Baker, and Shoba Ranganathan vii

6 viii Contents 14 Network Tools for the Analysis of Proteomic Data David Chisanga, Shivakumar Keerthikumar, Suresh Mathivanan, and Naveen Chilamkurti 15 Determining the Significance of Protein Network Features and Attributes Using Permutation Testing Joseph Cursons and Melissa J. Davis 16 Bioinformatics Tools and Resources for Analyzing Protein Structures Jason J. Paxman and Begoña Heras 17 In Silico Approach to Identify Potential Inhibitors for Axl- Gas6 Signaling Swathik Clarancia Peter, Jayakanthan Mannu, and Premendu P. Mathur Index

7 Contributors Seong Beom Ahn Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia Sushma Anand Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia Ching-Seng Ang The Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia Mark S. Baker Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia Joel Chick Department of Cell Biology, Harvard Medical School, Boston, MA, USA Naveen Chilamkurti Department of Computer Science and Information Technology, School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, VIC, Australia David Chisanga Department of Computer Science and Information Technology, School of Engineering and Mathematical Sciences, La Trobe University, Bundoora, VIC, Australia Brett Cooke Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia Joseph Cursons Systems Biology Laboratory, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC, Australia; ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC, Australia Debasis Dash G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India Melissa J. Davis Systems Biology Laboratory, Melbourne School of Engineering, The University of Melbourne, Parkville, VIC, Australia; Bioinformatics Division, Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia; Faculty of Medicine, Dentistry and Health Science, Department of Biochemistry and Molecular Biology, The University of Melbourne, Parkville, VIC, Australia Kevin M. Downard Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia; Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia Criselda Santan Fernandes Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia Harsha Gowda Institute of Bioinformatics, Bangalore, India; YU-IOB Center for Systems Biology and Molecular Medicine, Yenepoya University, Mangalore, India Paul Haynes Faculty of Medicine and Health Sciences, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia Begoña Heras Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia Michelle M. Hill The University of Queensland, Diamantina Institute, Translational Research Institute, Woolloongabba, QLD, Australia ix

8 x Contributors Mohammad Tawhidul Islam Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia Shivakumar Keerthikumar Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia Dhirendra Kumar G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India Shiyong Ma Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia; Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia Jayakanthan Mannu Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India Lennart Martens Medical Biotechnology Center, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium Suresh Mathivanan Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia Premendu P. Mathur School of Biotechnology, KIIT University, Bhubaneswar, India Geoffrey J. McLachlan School of Mathematics and Physics, The University of Queensland, St. Lucia, QLD, Australia Mehdi Mirzaei Faculty of Medicine and Health Sciences, Department of Chemistry and Biomolecular Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia Abidali Mohamedali Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, Australia Mark P. Molloy Faculty of Medicine and Health Sciences, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia; Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia Ishmam Nawar Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia Hien D. Nguyen School of Mathematics and Physics, The University of Queensland, St. Lucia, QLD, Australia; The University of Queensland, Diamantina Institute, Translational Research Institute, Woolloongabba, QLD, Australia Dana Pascovici Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia Krishna Patel Institute of Bioinformatics, Bangalore, India; Amrita School of Biotechnology, Kollam, India Mohashin Pathan Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia Jason J. Paxman Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, VIC, Australia Swathik Clarancia Peter Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India

9 Contributors xi Shoba Ranganathan Department of Chemistry and Biomolecular Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, NSW, Australia Monisha Samuel Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC, Australia Manika Singh Institute of Bioinformatics, Bangalore, India; Amrita School of Biotechnology, Amrita Kollam, India Elien Vandermarliere Medical Biotechnology Center, VIB, Ghent, Belgium; Department of Biochemistry and Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium Jason W.H. Wong Prince of Wales Clinical School, University of New South Wales, Sydney, NSW, Australia; Lowy Cancer Research Centre, University of New South Wales, Sydney, NSW, Australia Jemma X. Wu Department of Chemistry and Biomolecular Sciences, Australian Proteome Analysis Facility, Macquarie University, Sydney, NSW, Australia Yunqi Wu Faculty of Medicine and Health Sciences, Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia Amit Kumar Yadav G.N. Ramachandran Knowledge Centre for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, Delhi, India Şule Yılmaz Medical Biotechnology Center, VIB, Ghent, Belgium; Department of Biochemistry, Ghent University, Ghent, Belgium; Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium