Calculates false discovery rate estimates on crosslink identifications.

This tool calculates and FDR estimate for crosslink identifications, which are produced by OpenPepXL. The method employed currently is identical to the target-decoy approach used by xProphet (Walzthoeni et al., 2012). Consequently, this tool can also consume xquest.xml files (produced either by OpenPepXL or xQuest). The tool supports output in the idXML and mzIdentML formats.

pot. predecessor tools	→ XFDR →	pot. successor tools
OpenPepXL		OpenPepXLLF	-

The command line parameters of this tool are:

XFDR -- Calculates false discovery rate estimates on crosslink identifications
Full documentation: http://www.openms.de/doxygen/release/3.3.0/html/TOPP_XFDR.html
Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65
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:
  XFDR <options>

Options (mandatory options marked with '*'):
  -in <file>                       Crosslink Identifications in either xquest.xml, idXML, or mzIdentML format
                                    (as produced by OpenPepXL) (valid formats: 'xml', 'idXML', 'mzid', 'xques
                                   t.xml')
  -in_type <in_type>               Type of input file provided with -in. If omitted, the file type is guessed
                                    from the file extension. (valid: 'xml', 'idXML', 'mzid', 'xquest.xml')
  -out_idXML <idXML_file>          Output as idXML file (valid formats: 'idXML')
  -out_mzIdentML <mzIdentML_file>  Output as mzIdentML file (valid formats: 'mzid')
  -out_xquest <xQuestXML_file>     Output as xquest.xml file (valid formats: 'xquest.xml')
  -decoy_string <text>             Prefix of decoy protein ids. The correspondig target protein id should be 
                                   retrievable by deleting this prefix. (default: 'DECOY_')
  -minborder <value>               Filter for minimum precursor mass error (ppm) before FDR estimation. Value
                                   s outside of the tolerance window of the original search will effectively 
                                   disable this filter. (default: '-50.0')
  -maxborder <value>               Filter for maximum precursor mass error (ppm) before FDR estimation. Value
                                   s outside of the tolerance window of the original search will effectively 
                                   disable this filter. (default: '50.0')
  -mindeltas <value>               Filter for delta score, 0 disables the filter. Minimum delta score require
                                   d, hits are rejected if larger or equal. The delta score is a ratio of 
                                   the score of a hit and the score of the next best hit to the same spectrum
                                   , so the value range is between 0 and 1 with 1.0 meaning the scores are 
                                   equal and 0.5 meaning the next best score is half as high as the current 
                                   one. (default: '0.0') (min: '0.0' max: '1.0')
  -minionsmatched <number>         Filter for minimum matched ions per peptide. (default: '0') (min: '0')
  -uniquexl                        Calculate statistics based only on unique IDs. For a set of IDs from equal
                                    candidates (same pair of peptides, modifications and cross-linked positio
                                   ns), only the highest scoring hit will be considered. By default the score
                                    distribution will be estimated using all 1st ranked candidates.
  -no_qvalues                      Do not transform simple FDR to q-values
  -minscore <value>                Minimum score to be considered for FDR calculation. A number lower than 
                                   the lowest score will effectively disable this filter. (default: '-10.0')
  -binsize <value>                 Bin size for the cumulative histograms for score distributions. Should be 
                                   about the same size as the smallest expected difference between scores. 
                                   Smaller numbers will make XFDR more robust, but much slower. Negative numb
                                   ers are not allowed. Should only be changed if the range of the main score
                                    changes or another score than the OpenPepXL score is used. (default: '1.0
                                   e-04') (min: '1.0e-15')
                                   
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

+XFDRCalculates false discovery rate estimates on crosslink identifications

version3.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'XFDR'

in Crosslink Identifications in either xquest.xml, idXML, or mzIdentML format (as produced by OpenPepXL)input file*.xml, *.idXML, *.mzid, *.xquest.xml

in_type Type of input file provided with -in. If omitted, the file type is guessed from the file extension.xml, idXML, mzid, xquest.xml

out_idXML Output as idXML fileoutput file*.idXML

out_mzIdentML Output as mzIdentML fileoutput file*.mzid

out_xquest Output as xquest.xml fileoutput file*.xquest.xml

decoy_stringDECOY_ Prefix of decoy protein ids. The correspondig target protein id should be retrievable by deleting this prefix.

minborder-50.0 Filter for minimum precursor mass error (ppm) before FDR estimation. Values outside of the tolerance window of the original search will effectively disable this filter.

maxborder50.0 Filter for maximum precursor mass error (ppm) before FDR estimation. Values outside of the tolerance window of the original search will effectively disable this filter.

mindeltas0.0 Filter for delta score, 0 disables the filter. Minimum delta score required, hits are rejected if larger or equal. The delta score is a ratio of the score of a hit and the score of the next best hit to the same spectrum, so the value range is between 0 and 1 with 1.0 meaning the scores are equal and 0.5 meaning the next best score is half as high as the current one.0.0:1.0

minionsmatched0 Filter for minimum matched ions per peptide.0:∞

uniquexlfalse Calculate statistics based only on unique IDs. For a set of IDs from equal candidates (same pair of peptides, modifications and cross-linked positions), only the highest scoring hit will be considered. By default the score distribution will be estimated using all 1st ranked candidates.true, false

no_qvaluesfalse Do not transform simple FDR to q-valuestrue, false

minscore-10.0 Minimum score to be considered for FDR calculation. A number lower than the lowest score will effectively disable this filter.

binsize1.0e-04 Bin size for the cumulative histograms for score distributions. Should be about the same size as the smallest expected difference between scores. Smaller numbers will make XFDR more robust, but much slower. Negative numbers are not allowed. Should only be changed if the range of the main score changes or another score than the OpenPepXL score is used.1.0e-15:∞

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