Data Mining in Proteomics

by Hamacher, Michael; Eisenacher, Martin; Stephan, Christian

• ISBN13: 9781607619864
• ISBN10: 1607619865
• Format: Hardcover
• Copyright: 2010-12-08
• Publisher: Humana Pr Inc

Summary

Through the rapid development of proteomics methods and technologies, an enormous amount of data was created, leading to a wide-spread rethinking of strategy design and data interpretation. In Data Mining in Proteomics: From Standards to Applications, experts in the field present these new insights within the proteomics community, taking the historical evolution as well as the most important international standardization projects into account. Along with basic and sophisticated overviews of proteomics technologies, standard data formats, and databases, the volume features chapters on data interpretation strategies including statistics, spectra interpretation, and analysis environments as well as specialized tasks such as data annotation, peak picking, phosphoproteomics, spectrum libraries, LC/MS imaging, and splice isoforms. As a part of the highly successful Methods in Molecular Biology'„¢ series, this work provides the kind of detailed description and implementation advice that is crucial for getting optimal results.Authoritative and cutting-edge, Data Mining in Proteomics: From Standards to Applications is a well-balanced compendium for beginners and experts, offering a broad scope of data mining topics but always focusing on the current state-of-the-art and beyond.

Table of Contents

Preface	p. v
Contributors	p. ix
Data Generation and Result Finding
Instruments and Methods in Proteomics	p. 3
In-Depth Protein Characterization by Mass Spectrometry	p. 27
Analysis of Phosphoproteomics Data	p. 41
Databases
The Origin and Early Reception of Sequence Databases	p. 61
Laboratory Data and Sample Management for Proteomics	p. 79
PRIDE and "Database on Demand" as Valuable Tools for Computational Proteomics	p. 93
Analysing Proteomics Identifications in the Context of Functional and Structural Protein Annotation: Integrating Annotation Using PICR, DAS, and BioMart	p. 107
Tranche Distributed Repository and ProteomeCommons.org	p. 123
Standards
Data Standardization by the HUPO-PSI: How has the Community Benefitted?	p. 149
mzIdentML: An Open Community-Built Standard Format for the Results of Proteomics Spectrum Identification Algorithms	p. 161
Spectra, Chromatograms, Metadata: mzML-The Standard Data Format for Mass Spectrometer Output	p. 179
imzML: Imaging Mass Spectrometry Markup Language: A Common Data Format for Mass Spectrometry Imaging	p. 205
Tandem Mass Spectrometry Spectral Libraries and Library Searching	p. 225
Processing And Interpretation of Data
Inter-Lab Proteomics: Data Mining in Collaborative Projects on the Basis of the HUPO Brain Proteome Project's Pilot Studies	p. 235
Data Management and Data Integration in the HUPO Plasma Proteome Project	p. 247
Statistics in Experimental Design, Preprocessing, and Analysis of Proteomics Data	p. 259
The Evolution of Protein Interaction Networks	p. 273
Cytoscape: Software for Visualization and Analysis of Biological Networks	p. 291
Text Mining for Systems Modeling	p. 305
Identification of Alternatively Spliced Transcripts Using a Proteomic Informatics Approach	p. 319
Distributions of Ion Series in ETD and CID Spectra: Making a Comparison	p. 327
Tools
Evaluation of Peak-Picking Algorithms for Protein Mass Spectrometry	p. 341
OpenMS and TOPP: Open Source Software for LC-MS Data Analysis	p. 353
LC/MS Data Processing for Label-Free Quantitative Analysis	p. 369
Modelling and Systems Biology
Spectral Properties of Correlation Matrices - Towards Enhanced Spectral Clustering	p. 381
Standards, Databases, and Modeling Tools in Systems Biology	p. 413
Modeling of Cellular Processes: Methods, Data, and Requirements	p. 29
Index	p. 449
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