Tool to score phosphorylation sites of peptides.

pot. predecessor tools	→ PhosphoScoring →	pot. successor tools
CometAdapter (or other ID engines)	→ PhosphoScoring →	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/doxygen/nightly/html/TOPP_PhosphoScoring.html
Version: 3.6.0-pre-nightly-2026-03-06 Mar  7 2026, 01:46:19, Revision: c92c980
To cite OpenMS:
 + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec
   trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7.

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 (valid format
                                    s: 'idXML')
  -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

This section lists all parameters supported by the tool. Parameters are organized into hierarchical subsections that group related settings together. Subsections may contain further subsections or individual parameters.

Each parameter entry contains the following information:

Name The identifier used in configuration files and on the command line.
Default value The value used if the parameter is not explicitly specified.
Description A short explanation describing the purpose and behavior of the parameter.
Tags Additional metadata associated with the parameter.
Restrictions Allowed value ranges for numeric parameters or valid options for string parameters.

Parameter tags provide additional information about how a parameter is used. Some tags indicate whether a parameter is required or intended for advanced configuration, while others may be used internally by OpenMS or workflow tools.

Parameters highlighted as required must be specified for the tool to run successfully. Parameters marked as advanced allow fine-tuning of algorithm behavior and are typically not needed for standard workflows.

+PhosphoScoringScores potential phosphorylation sites in order to localize the most probable sites.

version3.6.0-pre-nightly-2026-03-06 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 annotated with phosphorylation scoresoutput file*.idXML

fragment_mass_tolerance0.05 Fragment mass tolerance for spectrum comparisons0.0:∞

fragment_mass_unitDa Unit of fragment mass toleranceDa, ppm

max_peptide_length40 Restrict scoring to peptides with a length no greater than this value ('0' for 'no restriction')0:∞

max_num_perm16384 Maximum number of permutations a sequence can have to be processed ('0' for 'no restriction')0:∞

unambiguous_score1000 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)

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 Overrides tool-specific checkstrue, false

testfalse Enables the test mode (needed for internal use only)true, false