| OpenMS 2.5.0

PhosphoScoring

Tool to score phosphorylation sites of peptides.

pot. predecessor tools | PhosphoScoring | 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).

In the output the score of the peptide hit describes the peptide score, which is a weighted average of all ten scores of the selected peptide sequence. For each phosphorylation site an individual Ascore was calculated and listed as meta value of the peptide hit (e.g. AScore_1, AScore_2).

The Ascore results of this TOPP tool differs with the results of the Ascore calculation provided on the website, but it seems that the implementation according to Beausoleil et al. has some calculation errors. It is not possible to recalculate the Ascore using the cumulative binomial probability formula with the given values (see Fig. 3c). In addition the site determining ions calculation seems not reliable, because in some test cases more site determining ions were calculated than it could be possible.

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.

    Full documentation: http://www.openms.de/documentation/TOPP_PhosphoScoring.html

    Version: 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Sep 10 2020, 12:20:39, Revision: GIT-NOTFOUND

    To cite OpenMS:

      Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959.

    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 concatenated

                                        sequence database (valid formats: 'idXML')

      -out <file>*                      Identification output annotated with phosphorylation scores

      -fragment_mass_tolerance <value>  Fragment mass tolerance for spectrum comparisons (default: '0.05' min:

                                        '0.0')

      -fragment_mass_unit <choice>      Unit of fragment mass tolerance (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 (default:

                                        '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
+PhosphoScoring Scores potential phosphorylation sites in order to localize the most probable sites.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'PhosphoScoring'
in Input file with MS/MS spectra input file*.mzML
id Identification input file which contains a search against a concatenated sequence database input file*.idXML
out Identification output annotated with phosphorylation scores output file
fragment_mass_tolerance 0.05 Fragment mass tolerance for spectrum comparisons 0.0:∞
fragment_mass_unit Da Unit of fragment mass tolerance Da,ppm
max_peptide_length 40 Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')0:∞
max_num_perm 16384 Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')0:∞
unambiguous_score 1000 Score to use for unambiguous assignments, where all sites on a peptide are phosphorylated. (Note: If a peptide is not phosphorylated at all, its score is set to '-1'.)
log Name of log file (created only when specified)
debug 0 Sets the debug level
threads 1 Sets the number of threads allowed to be used by the TOPP tool
no_progress false Disables progress logging to command line true,false
force false Overwrite tool specific checks.true,false
test false Enables the test mode (needed for internal use only)true,false