Bioinformatics for comparative proteomics / edited by Cathy H. Wu, Chuming Chen. — [New York] : Humana, c2011. – (58.17/M592/v.694)

Contents

    CONTENTS
    
    Preface
    Contributors
    PART I: BIOINFORMATICS FRAMEWORK FOR COMPARATIVE PROTEOMICS
    1 Protein Bioinformatics Databases and Resources
    2 A Guide to UniProt for Protein Scientists
    3 InterPro Protein Classification
    4 Reactome Knowledgebase of Human Biological Pathways and Processes
    5 eFIP: A Tool for Mining Functional Impact of Phosphorylation from Literature
    6 A Tutorial on Protein Ontology Resources for Proteomic Studies
    7 Structure-Guided Rule-Based Annotation of Protein Functional Sites in UniProt Knowledgebase
    PART II: PROTEOMIC BIOINFORMATICS
    8 Modeling Mass Spectrometry-Based Protein Analysis 109
    9 Protein Identification from Tandem Mass Spectra by Database Searching
    10 LC-MS Data Analysis for Differential Protein Expression Detection
    11 Protein Identification by Spectral Networks Analysis
    12 Software Pipeline and Data Analysis for MS/MS Proteomics: The Trans-Proteomic Pipeline
    13 Analysis of High-Throughput ELISA Microarray Data
    14 Proteomics Databases and Repositories
    15 Preparing Molecular Interaction Data for Publication
    16 Submitting Proteomics Data to PRIDE Using PRIDE Converter
    17 Automated Data Integration and Determination of Posttranslational Modifications with the Protein Inference Engine
    18 An Integrated Top-Down and Bottom-Up Strategy for Characterization of Protein Isoforms and Modifications
    PART III: COMPARATIVE PROTEOMICS IN SYSTEMS BIOLOGY
    19 Phosphoproteome Resource for Systems Biology Research
    20 Protein-Centric Data Integration for Functional Analysis of Comparative Proteomics Data
    21 Integration of Proteomic and Metabolomic Profiling as well as Metabolic Modeling for the Functional Analysis of Metabolic Networks
    22 Time Series Proteome Profiling
    Index