Part I: Data Generation and Result Finding1. Instruments and Methods in ProteomicsCaroline May, Frederic Brosseron, Piotr Chartowski, Cornelia Schumbrutzki, Bodo Schoenebeck, and Katrin Marcus2. In-Depth Protein Characterization by Mass SpectrometryDaniel Chamrad, Gerhard Körting, and Martin Blüggel3. Analysis of Phosphoproteomics DataChristoph SchaabPart II: Databases4. The Origin and Early Reception of Sequence DatabasesJoel B. Hagen5. Laboratory Data and Sample Management for ProteomicsJari Häkkinen and Fredrik Levander6. PRIDE and 'Database on Demand' as Valuable Tools for Computational ProteomicsJuan Antonio Vizcaíno, Florian Reisinger, Richard Côté, and Lennart Martens7. Analyzing Proteomics Identifications in the Context of Functional and Structural Protein Annotation: Integrating Annotation Using PICR, DAS, and BioMartPhilip Jones8. Tranche Distributed Repository and ProteomeCommons.orgBryan E. Smith, James A. Hill, Mark A. Gjukich, and Philip C. AndrewsPart III: Standards9. Data Standardization by the HUPO-PSI: How Has the Community Benefitted?Sandra Orchard and Henning Hermjakob10. mzIdentML: An Open Community-Built Standard Format for the Results of Proteomics Spectrum Identification AlgorithmsMartin Eisenacher11. Spectra, Chromatograms, Metadata: mzML - The Standard Data Format for Mass Spectrometer OutputMichael Turewicz and Eric W. Deutsch12. imzML: Imaging Mass Spectrometry Markup Language - A Common Data Format for Mass Spectrometry ImagingAndreas Römpp, Thorsten Schramm, Alfons Hester, Ivo Klinkert, Jean-Pierre Both, Ron M.A. Heeren, Markus Stöckli, and Bernhard Spengler13. Tandem Mass Spectrometry Spectral Libraries and Library SearchingEric W. DeutschPart IV: Processing and Interpretation of Data14. Inter-Lab Proteomics: Data Mining in Collaborative Projects on the Basis of the HUPO Brain Proteome Project´s Pilot StudiesMichael Hamacher, Bernd Gröttrup, Martin Eisenacher, Katrion Marcus, Young Mok Park, Helmut E. Meyer, and Christian Stephan15. Data Management and Data Integration in the HUPO Plasma Proteome ProjectGilbert S. Omenn16. Statistics in Experimental Design, Preprocessing, and Analysis of Proteomics DataKlaus Jung17. The Evolution of Protein Interaction NetworksAndreas Schüler and Erich Bornberg-Bauer18. Cytoscape: Software for Visualization and Analysis of Biological NetworksMichael Kohl, Sebastian Wiese, and Bettina Warscheid19. Text Mining for Systems ModellingAxel Kowald and Sebastian Schmeier20. Identification of Alternatively Spliced Transcripts Using a Proteomic Informatics ApproachRajasree Menon and Gilbert S. Omenn21. Distributions of Ion Series in ETD and CID Spectra: Making a ComparisonSarah R. Hart, King Wai Lau, Simon J. Gaskell, and Simon J. HubbardPart V: Tools22. Evaluation of Peak Picking Algorithms for Protein Mass SpectrometryChris Bauer, Rainer Cramer, and Johannes Schuchhardt23. OpenMS and TOPP: Open Source Software for LC-MS Data AnalysisAndreas Bertsch, Clemens Gröpl, Knut Reinert, and Oliver Kohlbacher24. LC/MS Data Processing for Label-Free Quantitative AnalysisPatricia M. Palagi, Markus Müller, Daniel Walther, and Frédérique LisacekPart VI: Modelling and Systems Biology25. Spectral Properties of Correlation Matrices: Towards Enhanced Spectral ClusteringDaniel Fulger and Enrico Scalas26. Standards, Databases, and Modeling Tools in Systems BiologyMichael Kohl27. Modelling of Cellular Processes: Methods, Data, and RequirementsThomas Millat, Olaf Wolkenhauer, Ralf-Jörg Fischer, and Hubert Bahl... Mehr
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