Tool to score phosphorylation sites of peptides.
pot. predecessor tools | ![]() ![]() | pot. successor tools |
MascotAdapter (or other ID engines) | PeptideIndexer |
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).
The command line parameters of this tool are:
PhosphoScoring -- Scores potential phosphorylation sites in order to localize the most probable sites. Version: 2.0.0 Aug 19 2015, 22:19:33, Revision: GIT-NOTFOUND Usage: PhosphoScoring <options> Options (mandatory options marked with '*'): -in <file> Input file with MS/MS spectra (valid formats: 'mzML') -id <file> Identification input file which contains a search against a concatena ted sequence database (valid formats: 'idXML') -out <file>* Identification output with annotated phosphorylation scores (valid formats: 'idXML') -fragment_mass_tolerance <tolerance> Fragment mass error (default: '0.05') -fragment_mass_unit <unit> Unit of fragment mass error (default: 'Da' valid: 'Da', 'ppm') Common TOPP options: -ini <file> Use the given TOPP INI file -threads <n> Sets the number of threads allowed to be used by the TOPP tool (defau lt: '1') -write_ini <file> Writes the default configuration file --help Shows options --helphelp Shows all options (including advanced)
INI file documentation of this tool:
OpenMS / TOPP release 2.0.0 | Documentation generated on Thu Aug 20 2015 01:44:31 using doxygen 1.8.9.1 |