Data mining in proteomics : from standards to applications / edited by Michael Hamacher, Martin Eisenacher and Christian Stephan. — New York, NY : Humana Press, c2011. – (58.17/M592/v.696)

Contents

    Contents
    
    Preface
    Contributors
    PART I DATA GENERATION AND RESULT FINDING
    1 Instruments and Methods in Proteomics
    2 In-Depth Protein Characterization by Mass Spectrometry
    3 Analysis of Phosphoproteomics Data
    PART II DATABASES
    4 The Origin and Early Reception of Sequence Databases
    5 Laboratory Data and Sample Management for Proteomics
    6 PRIDE and "Database on Demand" as Valuable Tools for Computational Proteomics
    7 Analysing Proteomics Identifications in the Context of Functional and Structural Protein Annotation: Integrating Annotation Using PICR， DAS， and BioMart
    8 Tranche Distributed Repository and ProteomeCommons.org 123
    PART III STANDARDS
    9 Data Standardization by the HUPO-PSI: How has the Community Benefitted?
    10 mzIdentML: An Open Community-Built Standard Format for the Results of Pr0teomics Spectrum Identification Algorithms
    11 Spectra， Chromatograms， Metadata: mzML-The Standard Data Format for Mass Spectrometer Output
    12 imzML: Imaging Mass Spectrometry Markup Language: A Common Data Format for Mass Spectrometry Imaging 205
    13 Tandem Mass Spectrometry Spectral Libraries and Library Searching 225
    PART IV PROCESSING AND INTERPRETATION OF DATA
    14 Inter-Lab Proteomics: Data Mining in Collaborative Projects on the Basis of the HUPO Brain Proteome Project's Pilot Studies 235
    15 Data Management and Data Integration in the HUPO Plasma Proteome Project
    16 Statistics in Experimental Design， Preprocessing， and Analysis of Proteomics Data 259
    17 The Evolution of Protein Interaction Networks 273
    18 Cytoscape: Software for Visualization and Analysis of Biological Networks
    19 Text Mining for Systems Modeling..
    20 Identification of Alternatively Spliced Transcripts Using a Proteomic Informatics Approach
    21 Distributions of Ion Series in ETD and CID Spectra: Making a Comparison
    PART V TOOLS
    22 Evaluation of Peak-Picking Algorithms for Protein Mass Spectrometry
    23 OpenMS and TOPP: Open Source Software for LC-MS Data Analysis
    24 LC/MS Data Processing for Label-Free Quantitative Analysis
    PART VI MODELLING AND SYSTEMS BIOLOGY
    25 Spectral Properties of Correlation Matrices - Towards Enhanced Spectral Clustering
    26 Standards， Databases， and Modeling Tools in Systems Biology
    27 Modeling of Cellular Processes: Methods， Data， and Requirements 429
    Index 449