蛋白质组学技术的飞速发展，催生了海量数据。这些数据的收集、存储、整理和分析给生物信息学带来了挑战。在这些方面，国内相关的生物信息学研究有了一定的研究基础，但在相关知识的普及教育方面非常欠缺，最明显的是国内尚没有一本蛋白质组信息学的专著。国内正需要这样一本深入浅出、全方位介绍比较蛋白质组数据处理的科学读本，能在基础与应用层面上起到指引的作用。但凡科学离不开技术，但凡数据离不开分析。特别在眼下生命科学研究组学化、组学研究系统化的大趋势下。国内蛋白质组学的瓶颈已不再是仪器和实验，而是实验设计和数据分析。引入吴、C.Chen编著的《比较蛋白质组学的生物信息学（影印版）》对加强、提升我国蛋白组学数据分析能力，着力于突破目前的瓶颈会起到巨大的推动作用。

随着生命科学和临床应用蛋白质组学技术的快速发展，许多生物信息学的研究方法、数据库、软件工具已经可以用于支持比较蛋白质组学的研究。吴、C.Chen编著的《比较蛋白质组学的生物信息学（影印版）》分为3个主要部分，包括与比较蛋白质组学相关的基础生物信息学框架、蛋白质组学数据分析的生物信息学数据库和工具，以及在系统生物学背景下的比较蛋白质组学关于整合生物信息的系统学和研究方法。《比较蛋白质组学的生物信息学（影印版）》提供了详细的操作建议，逐步地描述操作过程，务求让使用者在实验室获得最佳的实验结果。

全面且易于使用的《比较蛋白质组学的生物信息学》一书适合所有想要了解最先进的生物信息学数据库和工具、最新的蛋白质组学的计算方法和数据分析的未来发展趋势，以及系统生物学中的比较蛋白质组学研究的所有读者参考。

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