Proteome bioinformatics / edited by Simon J. Hubbard, Andrew R. Jones. — New York : Springer, 2010. – (58.17/M592/v.604)

Contents

    Contents
    
    Preface
    Contributors
    1 An Introduction to Proteome Bioinformatics
    2 Bioinformatics Methods for Protein Identification Using Peptide
    Mass Fingerprinting
    3 Computational Approaches to Peptide Identification via Tandem MS
    4 Scoring and Validation of Tandem MS Peptide Identification Methods
    5 Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics
    6 Understanding and Exploiting Peptide Fragment loll Intensities Using Experimental and Informatic Approaches
    7 Spectral Library Searching for Peptide Identification via Tandem MS ..
    8 De Novo Sequencing Methods in Proteomics 105
    9 Cross Species Proteomics 123
    10 Gene Model Detection Using Mass Spectrometry
    11 Signal Processing in Proteomics 145
    12 A High-Performance Reconfigurable Computing Solution for Peptide Mass Fingerprinting 163
    13 Mining Proteomic MS/MS Data for MRM Transitions
    14 OpenMS and TOPP: Open Source Software for LC-MS Data Analysis
    15 Trans-Proteomic Pipeline: A Pipeline for Proteomic Analysis
    16 Informatics and Statistics for Analyzing 2-D Gel Electrophoresis Images 239
    17 Automated Generic Analysis Tools for Protein Quantitation Using Stable Isotope Labeling 257
    18 An Overview of Label-Free Quantitation Methods in Proteomics by Mass Spectrometry 273
    19 The PeptideAtlas Project
    20 Using the PRIDE Proteomics Identifications Database for Knowledge Discovery and Data Analysis 297
    21 Molecular Interactions and Data Standardisation 309
    22 Mass Spectrometer Output File Format mzML 319
    23 Managing Experimental Data Using FuGE
    24 Proteomics Data Collection (ProDaC): Publishing and Collecting Proteomics Data Sets in Public Repositories Using Standard Formats 345
    25 Computational Resources for the Prediction and Analysis of Native Disorder in Proteins 369
    Index