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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:

PhosphoScoring -- Scores potential phosphorylation sites in order to localize the most probable sites.
Version: 2.0.0 Aug 25 2015, 00:02:58, 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:

Legend:
required parameter
advanced parameter
+PhosphoScoringScores potential phosphorylation sites in order to localize the most probable sites.
version2.0.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'PhosphoScoring'
in Input file with MS/MS spectrainput file*.mzML
id Identification input file which contains a search against a concatenated sequence databaseinput file*.idXML
out Identification output with annotated phosphorylation scoresoutput file*.idXML
fragment_mass_tolerance0.05 Fragment mass error
fragment_mass_unitDa Unit of fragment mass errorDa,ppm
log Name of log file (created only when specified)
debug0 Sets the debug level
threads1 Sets the number of threads allowed to be used by the TOPP tool
no_progressfalse Disables progress logging to command linetrue,false
forcefalse Overwrite tool specific checks.true,false
testfalse Enables the test mode (needed for internal use only)true,false

OpenMS / TOPP release 2.0.0 Documentation generated on Tue Aug 25 2015 05:53:56 using doxygen 1.8.9.1