Table of Contents Table of Contents Preface Contributors 1. An Introduction to Proteome Bioinformatics Andrew R. Jones and Simon J. Hubbard 2. Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting Zhao Song, Luonan Chen, and Dong Xu 3. Computational approaches to peptide identification via tandem MS Simon J. Hubbard 4. Scoring and validation of tandem MS peptide identification methods Markus Brosch and Jyoti Choudhary 5. Target-Decoy Search Strategy for Mass Spectrometry-based Proteomics Joshua E. Elias and Steven P. Gygi 6. Understanding and Exploiting Peptide Fragment Ion Intensities Using Experimental and Informatic Approaches Ashley C. Gucinski, Eric D. Dodds, Wenzhou Li, and Vicki H. Wysocki 7. Spectral Library Searching for Peptide Identification via Tandem MS Henry Lam and Ruedi Aebersold 8. De novo Sequencing Methods in Proteomics Christopher Hughes, Bin Ma, and Gilles A. Lajoie 9. Cross Species Proteomics J. C. Wright, R. J. Beynon, and S. J. Hubbard 10. Gene model detection using mass spectrometry Bindu Nanduri, Nan Wang, Mark L. Lawrence, Susan M. Bridges, and Shane C. Burgess 11. Signal Processing in Proteomics Rene Hussong and Andreas Hildebrandt 12. A High-Performance Reconfigurable Computing Solution for Peptide Mass Fingerprinting Daniel Coca and Istvan Bogdan 13. Mining proteomic MS/MS data for MRM transitions Jennifer A. Mead, Luca Bianco, and Conrad Bessant 14. OpenMS and TOPP: Open Source Software for LC-MS Data Analysis Knut Reinert and Oliver Kohlbacher 15. Trans-Proteomic Pipeline: A Pipeline For Proteomic Analysis Patrick G. A. Pedrioli 16. Informatics and statistics for analyzing 2-D gel electrophoresis images Andrew W. Dowsey, Jeffrey S. Morris, Howard B. Gutstein, and Guang-Zhong Yang 17. Automated generic analysis tools for protein quantitation using stable isotope labelling Wen-Lian Hsu and Ting-Yi Sung 18. An overview of label-free quantitation methods in proteomics by mass spectrometry Jason W.H. Wong and Gerard Cagney 19. The PeptideAtlas Project Eric W. Deutsch 20. Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data Analysis Philip Jones and Lennart Martens 21. Molecular Interactions and data standardisation Sandra Orchard and Samuel Kerrien 22. Mass Spectrometer Output File Format mzML Eric W. Deutsch 23. Managing experimental data using FuGE Andrew R. Jones and Allyson L. Lister 24. Proteomics Data Collection (ProDaC) - Publishing and Collecting Proteomics Data Sets in Public Repositories using Standard Formats Christian Stephan, Martin Eisenacher, Michael Kohl, and Helmut E. Meyer 25. Computational Resources for the Prediction and Analysis of Native Disorder in Proteins Melissa Pentony, Jonathan Ward, and David Jones
