| OpenMS 2.5.0

IDConflictResolver

Resolves ambiguous annotations of features with peptide identifications.

potential predecessor tools | IDConflictResolver | potential successor tools
IDMapper | TextExporter
FeatureLinkerUnlabeled (or another feature grouping algorithm) | ProteinQuantifier

The peptide identifications are filtered so that only one identification with a single hit (with the best score) is associated to each feature. (If two IDs have the same best score, either one of them may be selected.)

The the filtered identifications are added to the vector of unassigned peptides and also reduced to a single best hit.

This step may be useful before applying ProteinQuantifier, because features with ambiguous annotation are not considered for the quantification.

The command line parameters of this tool are:

    IDConflictResolver -- Resolves ambiguous annotations of features with peptide identifications

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

      IDConflictResolver <options>

    Options (mandatory options marked with '*'):

      -in <file>*                                           Input file (data annotated with identifications) (val

                                                            id formats: 'featureXML', 'consensusXML')

      -out <file>*                                          Output file (data with one peptide identification

                                                            per feature) (valid formats: 'featureXML', 'consensus

                                                            XML')

      -resolve_between_features <resolve_between_features>  A map may contain multiple features with both identic

                                                            al (possibly modified i.e. not stripped) sequence

                                                            and charge state. The feature with the 'highest inten

                                                            sity' is very likely the most reliable one. When swit

                                                            ched on, the filter removes the sequence annotation

                                                            from the lower intensity features, thereby resolving

                                                            the multiplicity. Only the most reliable features

                                                            for each (possibly modified i.e. not stripped) sequen

                                                            ce maintain annotated with this peptide sequence.

                                                            (default: 'off' valid: 'off', 'highest_intensity')

    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
+IDConflictResolver Resolves ambiguous annotations of features with peptide identifications
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'IDConflictResolver'
in Input file (data annotated with identifications)input file*.featureXML,*.consensusXML
out Output file (data with one peptide identification per feature)output file*.featureXML,*.consensusXML
resolve_between_features off A map may contain multiple features with both identical (possibly modified i.e. not stripped) sequence and charge state. The feature with the 'highest intensity' is very likely the most reliable one. When switched on, the filter removes the sequence annotation from the lower intensity features, thereby resolving the multiplicity. Only the most reliable features for each (possibly modified i.e. not stripped) sequence maintain annotated with this peptide sequence.off,highest_intensity
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