Preface
Contributors
PART I： BIOINFORMATICS FRAMEWORK FOR COMPARATIVE PROTEOMICS
1 Protein Bioinformatics Databases and Resources
Churning Chen， Hongzhan Huang， and Cathy H． Wu
2 A Guide to UniProt for Protein Scientists
Claire O'Donovan and Rolf Apweiler
3 InterPro Protein Classification
Jennifer McDowall and Sarah Hunter
4 Reactome Knowledgebase of Human Biological
Pathways and Processes
Peter D'Eustachio
5 eFIP： A Tool for Mining Functional Impact
of Phosphorylation from Literature
Cecilia N． Arighi， Amy Y． Siu， Catalina O． Tudor，
Jules A． Nchoutrnboube， Cathy It． Wu， and Vijay K． Shanker
6 A Tutorial on Protein Ontology Resources for Proteomic Studies
Cecilia N． Arighi
7 Structure-Guided Rule-Based Annotation． of Protein
Functional Sites in UniProt Knowledgebase
Sona Vasudevan， C．R． Vinayaka， Darren A． Natale，
Hongzhan Huang， Robel Y． Kahsay， and Cathy H． Wu
PART II： PROTEOMIC BIOINFORMATICS
8 Modeling Mass Spectrometry-Based Protein Analysis
Jan Eriksson and David Feny
9 Protein Identification from Tandem Mass Spectra
by Database Searching
Nathan J． Edwards
10 LC-MS Data Analysis for Differential
Protein Expression Detection
Rency S． Varghese and Habtorn W． Ressom
11 Protein Identification by Spectral Networks Analysis
Nuno Bandeira
12 Software Pipeline and Data Analysis for MS/MS Proteomics：
The Trans-Proteomic Pipeline
Andrew Keller and David Shteynberg
13 Analysis of High-Throughput ELISA Microarray Data
Amanda M． White， Don S． Daly， and Richard C． Zangar
14 Proteomics Databases and Repositories
Lennart Martens
15 Preparing Molecular Interaction Data for Publication
Sandra Orchard and Henning Hermjakob
16 Submitting Proteomics Data to PRIDE Using PRIDE Converter
Harald Barsnes， Juan Antonio Vizcalno， Florian Reisinger，
Ingvar Eidhammer， and Lennart Martens
17 Automated Data Integration and Determination of
Posttranslational Modifications with the Protein Inference Engine
Stuart R． Jefferys and Morgan C． Giddings
18 An Integrated Top-Down and Bottom-Up Strategy
for Characterization of Protein Isoforms and Modifications
Si Wu， Nikola Toli， Zhixin Tian， Errol W． Robinson，
and Ljiljana Paa- Toli
PART III： COMPARATIVE PROTEOMICS IN SYSTEMS BIOLOGY
19 Phosphoproteome Resource for Systems Biology Research
Bernd Bodenmiller and Ruedi Aebersold
20 Protein-Centric Data Integration for Functional Analysis of
Comparative Proteomics Data
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
Patrick May， Nils Christian， Oliver Ebenhh，
Wolfram Weckwerth， and Dirk Walther
22 Time Series Proteome Profiling
Catherine A． Formolo， Michelle Mint4 Asako Takanohashi，
Kristy J． Brown， Adeline Vanderver， Brian Halligan，
and Yetrib Hathout
Index
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