Bioinformatics for Comparative Proteomics

by Wu, Cathy H.; Chen, Chuming

• ISBN13: 9781607619765
• ISBN10: 1607619768
• Format: Hardcover
• Copyright: 2010-11-19
• Publisher: Humana Pr Inc

Summary

With the rapid development of proteomic technologies in the life sciences and in clinical applications, many bioinformatics methodologies, databases, and software tools have been developed to support comparative proteomics study. In Bioinformatics for Comparative Proteomics, experts in the field highlight the current status, challenges, open problems, and future trends for developing bioinformatics tools and resources for comparative proteomics research in order to deliver a definitive reference providing both the breadth and depth needed on the subject. Structured in three major sections, this detailed volume covers basic bioinformatics frameworks relating to comparative proteomics, bioinformatics databases and tools for proteomics data analysis, and integrated bioinformatics systems and approaches for studying comparative proteomics in the systems biology context. Written for the highly successful Methods in Molecular Biology'„¢ series, the contributions in this book provide the meticulous, step-by-step description and implementation advice that is crucial for getting optimal results in the lab.Comprehensive and easy-to-use, Bioinformatics for Comparative Proteomics serves all readers who wish to learn about state-of-the-art bioinformatics databases and tools, novel computational methods and future trends in proteomics data analysis, and comparative proteomics in systems biology.

Table of Contents

Preface	p. v
Contributors	p. xi
Bioinformatics Framework for Comparative Proteomics
Protein Bioinformatics Databases and Resources	p. 3
A Guide to UniProt for Protein Scientists	p. 25
InterPro Protein Classification	p. 37
Reactome Knowledgebase of Human Biological Pathways and Processes	p. 49
eFIP: A Tool for Mining Functional Impact of Phosphorylation from Literature	p. 63
A Tutorial on Protein Ontology Resources for Proteomic Studies	p. 77
Structure-Guided Rule-Based Annotation of Protein Functional Sites in UniProt Knowledgebase	p. 91
Proteomic Bioinformatics
Modeling Mass Spectrometry-Based Protein Analysis	p. 109
Protein Identification from Tandem Mass Spectra by Database Searching	p. 119
LC-MS Data Analysis for Differential Protein Expression Detection	p. 139
Protein Identification by Spectral Networks Analysis	p. 151
Software Pipeline and Data Analysis for MS/MS Proteomics: The Trans-Proteomic Pipeline	p. 169
Analysis of High-Throughput ELISA Microarray Data	p. 191
Proteomics Databases and Repositories	p. 213
Preparing Molecular Interaction Data for Publication	p. 229
Submitting Proteomics Data to PRIDE Using PRIDE Converter	p. 237
Automated Data Integration and Determination of Posttranslational Modifications with the Protein Inference Engine	p. 255
An Integrated Top-Down and Bottom-Up Strategy for Characterization of Protein Isoforms and Modifications	p. 293
Comparative Proteomics in Systems Biology
Phosphoproteome Resource for Systems Biology Research	p. 307
Protein-Centric Data Integration for Functional Analysis of Comparative Proteomics Data	p. 323
Integration of Proteomic and Metabolomic Profiling as well as Metabolic Modeling for the Functional Analysis of Metabolic Networks	p. 341
Time Series Proteome Profiling	p. 365
Index	p. 379
Table of Contents provided by Ingram. All Rights Reserved.