Data mining in proteomics : from standards to applications
Author(s)
Bibliographic Information
Data mining in proteomics : from standards to applications
（Methods in molecular biology / John M. Walker, series editor, 696）（Springer protocols）
Humana Press : Springer Science : Business Media, c2011
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Includes bibliographical references and index
Description and Table of Contents
Description
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 (TM) 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
Part I: Data Generation and Result Finding
1. Instruments and Methods in Proteomics
Caroline May, Frederic Brosseron, Piotr Chartowski, Cornelia Schumbrutzki, Bodo Schoenebeck, and Katrin Marcus
2. In-Depth Protein Characterization by Mass Spectrometry
Daniel Chamrad, Gerhard Koerting, and Martin Bluggel
3. Analysis of Phosphoproteomics Data
Christoph Schaab
Part II: Databases
4. The Origin and Early Reception of Sequence Databases
Joel B. Hagen
5. Laboratory Data and Sample Management for Proteomics
Jari Hakkinen and Fredrik Levander
6. PRIDE and 'Database on Demand' as Valuable Tools for Computational Proteomics
Juan Antonio Vizcaino, Florian Reisinger, Richard Cote, and Lennart Martens
7. Analyzing Proteomics Identifications in the Context of Functional and Structural Protein Annotation: Integrating Annotation Using PICR, DAS, and BioMart
Philip Jones
8. Tranche Distributed Repository and ProteomeCommons.org
Bryan E. Smith, James A. Hill, Mark A. Gjukich, and Philip C. Andrews
Part III: Standards
9. Data Standardization by the HUPO-PSI: How Has the Community Benefitted?
Sandra Orchard and Henning Hermjakob
10. mzIdentML: An Open Community-Built Standard Format for the Results of Proteomics Spectrum Identification Algorithms
Martin Eisenacher
11. Spectra, Chromatograms, Metadata: mzML - The Standard Data Format for Mass Spectrometer Output
Michael Turewicz and Eric W. Deutsch
12. imzML: Imaging Mass Spectrometry Markup Language - A Common Data Format for Mass Spectrometry Imaging
Andreas Roempp, Thorsten Schramm, Alfons Hester, Ivo Klinkert, Jean-Pierre Both, Ron M.A. Heeren, Markus Stoeckli, and Bernhard Spengler
13. Tandem Mass Spectrometry Spectral Libraries and Library Searching
Eric W. Deutsch
Part IV: Processing and Interpretation of Data
14. Inter-Lab Proteomics: Data Mining in Collaborative Projects on the Basis of the HUPO Brain Proteome Projects Pilot Studies
Michael Hamacher, Bernd Groettrup, Martin Eisenacher, Katrion Marcus, Young Mok Park, Helmut E. Meyer, and Christian Stephan
15. Data Management and Data Integration in the HUPO Plasma Proteome Project
Gilbert S. Omenn
16. Statistics in Experimental Design, Preprocessing, and Analysis of Proteomics Data
Klaus Jung
17. The Evolution of Protein Interaction Networks
Andreas Schuler and Erich Bornberg-Bauer
18. Cytoscape: Software for Visualization and Analysis of Biological Networks
Michael Kohl, Sebastian Wiese, and Bettina Warscheid
19. Text Mining for Systems Modelling
Axel Kowald and Sebastian Schmeier
20. Identification of Alternatively Spliced Transcripts Using a Proteomic Informatics Approach
Rajasree Menon and Gilbert S. Omenn
21. Distributions of Ion Series in ETD and CID Spectra: Making a Comparison
Sarah R. Hart, King Wai Lau, Simon J. Gaskell, and Simon J. Hubbard
Part V: Tools
22. Evaluation of Peak Picking Algorithms for Protein Mass Spectrometry
Chris Bauer, Rainer Cramer, and Johannes Schuchhardt
23. OpenMS and TOPP: Open Source Software for LC-MS Data Analysis
Andreas Bertsch, Clemens Groepl, Knut Reinert, and Oliver Kohlbacher
24. LC/MS Data Processing for Label-Free Quantitative Analysis
Patricia M. Palagi, Markus Muller, Daniel Walther, and Frederique Lisacek
Part VI: Modelling and Systems Biology
25. Spectral Properties of Correlation Matrices: Towards Enhanced Spectral Clustering
Daniel Fulger and Enrico Scalas
26. Standards, Databases, and Modeling Tools in Systems Biology
Michael Kohl
27. Modelling of Cellular Processes: Methods, Data, and Requirements
Thomas Millat, Olaf Wolkenhauer, Ralf-Joerg Fischer, and Hubert Bahl
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