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，F(xiàn)lorian 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