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PhosphoScoring

Tool to score phosphorylation sites of peptides.

pot. predecessor tools $ \longrightarrow $ PhosphoScoring $ \longrightarrow $ pot. successor tools
MascotAdapter (or other ID engines) PeptideIndexer
Experimental classes:
This TOPP tool is not well tested and some features might not be working correctly.

This tool performs phosphorylation analysis and site localization. Input files are an LC-MS/MS data file as well as the corresponding identification file. Firstly, the peptide identifications are mapped onto the spectra. Secondly, the tool uses an implementation of the Ascore according to Beausoleil et al. in order to localize the most probable phosphorylation sites.

For details, see:
Beausoleil et al.: A probability-based approach for high-throughput protein phosphorylation analysis and site localization (Nat. Biotechnol., 2006, PMID: 16964243).

Note
Currently mzIdentML (mzid) is not directly supported as an input/output format of this tool. Convert mzid files to/from idXML using IDFileConverter if necessary.

The command line parameters of this tool are:

INI file documentation of this tool:


OpenMS / TOPP release 2.0.0 Documentation generated on Wed Dec 2 2015 19:41:33 using doxygen 1.8.9.1