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  • Book
    edited by Michael Hamacher, Martin Eisenacher and Christian Stephan.
    Digital : Springer2011
    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 -- Analysing 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 project's 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 modeling -- 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 -- Modeling of cellular processes: Methods, data, and requirements.