[内容简介]
随着蛋白质组学技术自身及其在生命科学与医学应用中的快速发展，许多生物信息学方法、数据库和软件被开发出来并成功用于比较蛋白质组学研究。在该书中，专家描述了相关领域中最新的现状、挑战、所面临的开放性问题、以及未来的发展趋势。该书内容涉及发展比较蛋白质组学研究所需的生物信息学工具和资源，为了解该领域提供了具有相当广度和深度的知识体系和引用参考。作为分子生物学方法?系列丛书，该书提供了细致的、步步渐进式的描述，以及在具体实施上的建议。这些对于在实验中获得理想的结果至关重要。该书内容全面、易于使用，对所有希望了解蛋白质组学数据分析和系统生物学层面上比较蛋白质组学的生物信息学数据库、工具、新计算方法及其未来发展趋势的读者都有所裨益
[目次]
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