Bioinformatics for Comparative Proteomics

Editors:

ISBN: 978-1-60761-976-5 (Print) 978-1-60761-977-2 (Online)

Table of contents (22 protocols)

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  1. Front Matter

    Pages i-xiii

  2. Bioinformatics Framework for Comparative Proteomics

    1. Front Matter

      Pages 1-1

    2. No Access

      Book Protocol

      Pages 3-24

      Protein Bioinformatics Databases and Resources

    3. No Access

      Book Protocol

      Pages 25-35

      A Guide to UniProt for Protein Scientists

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      Pages 37-47

      InterPro Protein Classification

    5. No Access

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      Pages 49-61

      Reactome Knowledgebase of Human Biological Pathways and Processes

    6. No Access

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      Pages 63-75

      eFIP: A Tool for Mining Functional Impact of Phosphorylation from Literature

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      Pages 77-90

      A Tutorial on Protein Ontology Resources for Proteomic Studies

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      Pages 91-105

      Structure-Guided Rule-Based Annotation of Protein Functional Sites in UniProt Knowledgebase

  3. Proteomic Bioinformatics

    1. Front Matter

      Pages 107-107

    2. No Access

      Book Protocol

      Pages 109-117

      Modeling Mass Spectrometry-Based Protein Analysis

    3. No Access

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      Pages 119-138

      Protein Identification from Tandem Mass Spectra by Database Searching

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      Pages 139-150

      LC-MS Data Analysis for Differential Protein Expression Detection

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      Pages 151-168

      Protein Identification by Spectral Networks Analysis

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      Pages 169-189

      Software Pipeline and Data Analysis for MS/MS Proteomics: The Trans-Proteomic Pipeline

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      Pages 191-211

      Analysis of High-Throughput ELISA Microarray Data

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      Pages 213-227

      Proteomics Databases and Repositories

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      Pages 229-236

      Preparing Molecular Interaction Data for Publication

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      Pages 237-253

      Submitting Proteomics Data to PRIDE Using PRIDE Converter

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      Pages 255-290

      Automated Data Integration and Determination of Posttranslational Modifications with the Protein Inference Engine

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      Pages 291-304

      An Integrated Top-Down and Bottom-Up Strategy for Characterization of Protein Isoforms and Modifications

  4. Comparative Proteomics in Systems Biology

    1. Front Matter

      Pages 305-305

    2. No Access

      Book Protocol

      Pages 307-322

      Phosphoproteome Resource for Systems Biology Research

    3. No Access

      Book Protocol

      Pages 323-339

      Protein-Centric Data Integration for Functional Analysis of Comparative Proteomics Data

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