Contents Preface Contributors xi PART I：BIOINFORMATICS FRAMEWORK FOR COMPARATIVE PROTEOMICS 1 Protein Bioinformatics Databases and Resources 3 Chuming Chen，Hongzhan Huang：and Cathy H. Wu 2 A Guide to UniProt for Protein Scientists 25 Claire O. Donolan and Rolf Apweiler 3 InterPro Protein Classification 37 Jennifer McDowall and Sarah Hunter 4 Reactome Knowledgebase of Human Biological Pathways and Processes 49 Peter D Eustachio 5 eFIP：A. Tool for Mining Functional Impact of Phosphorylation from Literature 63 Cecilia N. Arighi，Amy Y. Siu，Catalina O. Tudor，Jules A. Nchoutmboube，Cathy H. Wu，and Vijay K. Shanker 6 A Tutorial on Protein Ontology Resources for Proteomic Studies 77 Cecilia N. Arighi 7 Structure-Guided Rule-Based Annotation of Protein Functional Sites in UniProt Knowledgebase 91 Sona Vasudevan，C. R. Viayaka，Darren A. Natale，Hongzhan Huang：Robel Y Kahsay and Cathy H. Wu P ART II：PROTEOMIC BIOINFORMATICS 8 Modeling Mass Spectrometry-Based Protein Analysis 109 Jan Eriksson and Dalid Fenyo 9 Protein Identification from Tandem Mass Spectra by Database Searching 119 Nathan J. Edwards 10 LC-MS Data Analysis for Differential Protein Expression Detection 139 Rency S. Varghese and Habtom W. Ressom 11 Protein Identification by Spectral Networks Analysis 151 Nuno Bandeira 12 Software Pipeline and Data Analysis for MS/MS Proteomics：The Trans-Proteomic Pipeline 169 Andrew Keller and Dalid Shteynberg 13 Analysis of High-Throughput ELISA Microarray Data 191 Amanda M White，Don S Daly，and Richard C Zangar 14 Proteomics Databases and Repositories 213 Lennart Martens 15 Preparing Molecular Interaction Data for Publication 229 Sandra Orchard and Henning Hermjakob 16 Submitting Proteomics Data to PRIDE Using PRIDE Converter 237 Harald Barsnes，Juan Anwnio Vizcaino，Florian Reisinger，Ingvar Eidhammer，and Lennart Martens 17 Automated Data Integration and Determination of Posttranslational Modifications with the Protein Inference Engine 255 Stuart R Jefferys and Morgan C. Giddings 18 An Integrated Top-Down and Bottom-Up Strategy for Characterization of Protein Isoforms and Modifications 293 Si Wu，Nikola Tolil，Zhixin Tian，Errol W Robinson，and Ljiljana Pasa-Tolil PART III：COMPARATIVE PROTEOMICS IN SYSTEMS BIOLOGY 19 Phosphoproteome Resource for Systems Biology Research 307 Bernd Bodenmiller and Ruedi Aebersold 20 Protein-Centric Data Integration for Functional Analysis of Comparative Proteomics Data 323 Peter B McGarvey，Jian Zhang，Darren A Natale，Cathy H. Wu，and Hongzhan Huang 21 Integration of Proteomic and Metabolomic Profiling as well as Metabolic Modeling for the Functional Analysis of Metabolic Networks 341 Patrick May，Nils Christian，Oliver Ebenhob，Wolfram Weekwertb，and Dirk Walther 22 Time Series Proteome Profiling 365 Catherine A Formolo，Michelle Mintz，Asako Takanohashi，Kristy J Brown，Adeline Vanderver Brian Halligan，and Yetrib Hathout Index 379
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