Proteome Bioinformatics

Editors:

ISBN: 978-1-60761-443-2 (Print) 978-1-60761-444-9 (Online)

Table of contents (25 protocols)

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  1. Front Matter

    Pages i-xi

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    Pages 1-5

    An Introduction to Proteome Bioinformatics

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    Pages 7-22

    Bioinformatics Methods for Protein Identification Using Peptide Mass Fingerprinting

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    Pages 23-42

    Computational Approaches to Peptide Identification via Tandem MS

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    Pages 43-53

    Scoring and Validation of Tandem MS Peptide Identification Methods

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    Pages 55-71

    Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics

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    Pages 73-94

    Understanding and Exploiting Peptide Fragment Ion Intensities Using Experimental and Informatic Approaches

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    Pages 95-103

    Spectral Library Searching for Peptide Identification via Tandem MS

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    Pages 105-121

    De Novo Sequencing Methods in Proteomics

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    Pages 123-135

    Cross Species Proteomics

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    Pages 137-144

    Gene Model Detection Using Mass Spectrometry

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    Pages 145-161

    Signal Processing in Proteomics

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    Pages 163-185

    A High-Performance Reconfigurable Computing Solution for Peptide Mass Fingerprinting

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    Pages 187-199

    Mining Proteomic MS/MS Data for MRM Transitions

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    Pages 201-211

    OpenMS and TOPP: Open Source Software for LC-MS Data Analysis

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    Pages 213-238

    Trans-Proteomic Pipeline: A Pipeline for Proteomic Analysis

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    Pages 239-255

    Informatics and Statistics for Analyzing 2-D Gel Electrophoresis Images

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    Pages 257-272

    Automated Generic Analysis Tools for Protein Quantitation Using Stable Isotope Labeling

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    Pages 273-283

    An Overview of Label-Free Quantitation Methods in Proteomics by Mass Spectrometry

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    Pages 285-296

    The PeptideAtlas Project

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    Pages 297-307

    Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data Analysis

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