Bookedited by Michael Hamacher, Martin Eisenacher and Christian Stephan.
Contents:
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.