內容簡介
隨著蛋白質組學技術自身及其在生命科學與醫學應用中的快速發展,許多生物信息學方法、數據庫和軟件被開發齣來並成功用於比較蛋白質組學研究。在《新生物學叢書:比較蛋白質組學的生物信息學(影印版)》中,專傢描述瞭相關領域中最新的現狀、挑戰、所麵臨的開放性問題、以及未來的發展趨勢。《新生物學叢書:比較蛋白質組學的生物信息學(影印版)》內容涉及發展比較蛋白質組學研究所需的生物信息學工具和資源,為瞭解該領域提供瞭具有相當廣度和深度的知識體係和引用參考。這些對於在實驗中獲得理想的結果至關重要。《新生物學叢書:比較蛋白質組學的生物信息學(影印版)》內容全麵、易於使用,對所有希望瞭解蛋白質組學數據分析和係統生物學層麵上比較蛋白質組學的生物信息學數據庫、工具、新計算方法及其未來發展趨勢的讀者都有所裨益。
目錄
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
前言/序言
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