| OpenMS 2.5.0

IDDecoyProbability

Util to estimate probability of peptide hits

pot. predecessor tools | IDDecoyProbability | pot. successor tools
MascotAdapter (or other ID engines) | -
PeptideIndexer

Experimental classes:
  This util is deprecated and might behave not as expected!

So far an estimation of the false score distribution with a gamma distribution and the correct score distribution with a gaussian distribution is performed. The probabilities are calculated using bayes law, similar to PeptideProphet. This implementation is much simpler than that of PeptideProphet.

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:

    IDDecoyProbability -- Estimates peptide probabilities using a decoy search strategy.

    WARNING: This util is deprecated.

    Full documentation: http://www.openms.de/documentation/UTILS_IDDecoyProbability.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:

      IDDecoyProbability <options>

    This tool has algorithm parameters that are not shown here! Please check the ini file for a detailed descript

    ion or use the --helphelp option.

    Options (mandatory options marked with '*'):

      -in <file>         Identification input of combined forward decoy search (reindex with PeptideIndexer first

                         ) (valid formats: 'idXML')

      -fwd_in <file>     Identification input of forward run (valid formats: 'idXML')

      -rev_in <file>     Identification input of decoy run (valid formats: 'idXML')

      -out <file>*       Identification output with forward scores converted to probabilities (valid formats:

                         'idXML')

    Common UTIL 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)

    The following configuration subsections are valid:

     - decoy_algorithm   Algorithm parameter subsection

    You can write an example INI file using the '-write_ini' option.

    Documentation of subsection parameters can be found in the doxygen documentation or the INIFileEditor.

    For more information, please consult the online documentation for this tool:

      - http://www.openms.de/documentation/UTILS_IDDecoyProbability.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+IDDecoyProbability Estimates peptide probabilities using a decoy search strategy.
WARNING: This util is deprecated.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'IDDecoyProbability'
in Identification input of combined forward decoy search (reindex with PeptideIndexer first)input file*.idXML
fwd_in Identification input of forward run input file*.idXML
rev_in Identification input of decoy run input file*.idXML
out Identification output with forward scores converted to probabilities output file*.idXML
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
+++decoy_algorithm Algorithm parameter subsection
number_of_bins 40 Number of bins used for the fitting, if sparse datasets are used, this number should be smaller
lower_score_better_default_value_if_zero 50.0 This value is used if e.g. a E-value score is 0 and cannot be transformed in a real number (log of E-value)

For the parameters of the algorithm section see the algorithms documentation:
decoy_algorithm