Mass Spectrometry data requires multiple data analysis steps. First, the spectra need to be matched to theoretical peptides. False discovery rates for peptide spectral matches need to be calculated. The protein identifications need to be interpolated. Protein quantitation then needs to be determined. These tools have been compiled into pipelines, but can also be run separately.
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The Seattle Proteome Center (SPC) is committed to providing free, open-source, software projects in support of cutting-edge proteomics research.
ProteoWizard provides a set of open-source, cross-platform software libraries and tools (e.g. msconvert, Skyline, IDPicker, SeeMS) that facilitate proteomics data analysis.
The CRUX mass spectrometry analysis toolkit is an open source project that aims to provide users with a cross-platform suite of analysis tools for interpreting protein mass spectrometry data.
MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.