Title | Data Mining in Proteomics [electronic resource] : From Standards to Applications / edited by Michael Hamacher, Martin Eisenacher, Christian Stephan |
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Imprint | Totowa, NJ : Humana Press, 2011 |
Connect to | http://dx.doi.org/10.1007/978-1-60761-987-1 |
Descript | XII, 420 p. 145 illus., 2 illus. in color. online resource |
Instruments and Methods in Proteomics -- In-Depth Protein Characterization by Mass Spectrometry -- Analysis of Phosphoproteomics Data -- The Origin and Early Reception of Sequence Databases -- Laboratory Data and Sample Management for Proteomics -- PRIDE and ‘Database on Demand’ as Valuable Tools for Computational Proteomics -- Analyzing Proteomics Identifications in the Context of Functional and Structural Protein Annotation: Integrating Annotation Using PICR, DAS, and BioMart -- Tranche Distributed Repository and ProteomeCommons.org -- Data Standardization by the HUPO-PSI: How Has the Community Benefitted? -- mzIdentML: An Open Community-Built Standard Format for the Results of Proteomics Spectrum Identification Algorithms -- Spectra, Chromatograms, Metadata: mzML – The Standard Data Format for Mass Spectrometer Output -- imzML: Imaging Mass Spectrometry Markup Language – A Common Data Format for Mass Spectrometry Imaging -- Tandem Mass Spectrometry Spectral Libraries and Library Searching -- Inter-Lab Proteomics: Data Mining in Collaborative Projects on the Basis of the HUPO Brain Proteome Project́s Pilot Studies -- Data Management and Data Integration in the HUPO Plasma Proteome Project -- Statistics in Experimental Design, Preprocessing, and Analysis of Proteomics Data -- The Evolution of Protein Interaction Networks -- Cytoscape: Software for Visualization and Analysis of Biological Networks -- Text Mining for Systems Modelling -- Identification of Alternatively Spliced Transcripts Using a Proteomic Informatics Approach -- Distributions of Ion Series in ETD and CID Spectra: Making a Comparison -- Evaluation of Peak Picking Algorithms for Protein Mass Spectrometry -- OpenMS and TOPP: Open Source Software for LC-MS Data Analysis -- LC/MS Data Processing for Label-Free Quantitative Analysis -- Spectral Properties of Correlation Matrices: Towards Enhanced Spectral Clustering -- Standards, Databases, and Modeling Tools in Systems Biology -- Modelling of Cellular Processes: Methods, Data, and Requirements