:: DESCRIPTION
CHAMPS is software for computing the complete sequence of a protein from the tandem mass spectrometry data of multiple-enzyme digests of the protein.
::DEVELOPER
Xiaowen Liu ,CCMS The Center for Computational Mass Spectrometry
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
Luciphor2 is a site localization tool for generic post-translational modifications (PTMs) using tandem mass spectrometry data.
::DEVELOPER
Proteomics & Integrative Bioinformatics Lab
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2015 Apr 1;31(7):1141-3. doi: 10.1093/bioinformatics/btu788. Epub 2014 Nov 25.
LuciPHOr2: site localization of generic post-translational modifications from tandem mass spectrometry data.
Fermin D, Avtonomov D, Choi H, Nesvizhskii AI
:: DESCRIPTION
TPP (Trans-Proteomic Pipeline) is a mature suite of tools for mass-spec (MS, MS/MS) based proteomics: statistical validation, quantitation, visualization, and converters from raw MS data to our open mzXML format.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Methods Mol Biol. 2010;604:213-38. doi: 10.1007/978-1-60761-444-9_15.
Trans-proteomic pipeline: a pipeline for proteomic analysis.
Pedrioli PG.
:: DESCRIPTION
Proteomatic is a free data processing pipeline created for the purpose of evaluating mass spectrometric proteomics experiments. Functionality is provided via scripts, and these scripts can be chained together into a high-throughput data processing pipeline.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Proteomics to go: Proteomatic enables the user-friendly creation of versatile MS/MS data evaluation workflows
Specht M., Kuhlgert S., Fufezan C., Hippler M.
Bioinformatics (2011) 27(8): 1183-1184, doi: 10.1093/bioinformatics/btr081
:: DESCRIPTION
MSMS is a coalescent simulator that models itself off Hudsons ms in usage and includes selection. It is fast, often faster than ms, and portable running on Mac OSX, windows and Linux. By using this tool, one can study the patterns of selection in complicated demographic scenarios.
MSMSPlay is a GUI designed for simple exploration of basic population genetic theory. Its meant for exploratory runs with some useful output in an interactive fashion.
::DEVELOPER
The Mathematics and BioSciences Group
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Ewing G. and Hermisson J. (2010).
MSMS: A coalescent simulation program including recombination, demographic structure, and selection at a single locus.
Bioinformatics 26: 2064-2065.
:: DESCRIPTION
Fido uses a probability model to rank proteins according to the posterior probability of their presence in a complex mixture, based on evidence derived from a shotgun proteomics experiment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Oliver Serang et al.
Efficient Marginalization to Compute Protein Posterior Probabilities from Shotgun Mass Spectrometry Data
J. Proteome Res., 2010, 9 (10), pp 5346–5357
