| OpenMS 2.5.0

MultiplexResolver

Completes peptide multiplets and resolves conflicts within them.

pot. predecessor tools | MultiplexResolver | pot. successor tools
IDMapper | ProteinQuantifier
IDConflictResolver

Tools such as FeatureFinderMultiplex can detect peptide feature multiplets in labeled experimental data. The multiplets can then be annotated with peptide sequences using the IDMapper tool (*). The MultiplexResolver tool is consolidating these results in two steps.

- Any multiplets with conflicting quantitative and sequence information are filtered out. As example, let us consider a triple SILAC analyis. Let us assume a sequence "LDNLVAIFDINR(Label:13C(6)15N(4))" with a single Arg10 label is mapped to the light feature in a SILAC triplet. Either peptide feature detection or sequence information must be incorrect und the triplet is removed.
- In a second step, any incomplete peptide feature groups are completed with dummy features of zero intensity. As example, let us stay with the triple SILAC analysis. But let us now assume the sequence "LDNLVAIFDINR(Label:13C(6)15N(4))" is mapped to the heavy partner of a peptide feature pair. This is no conflict. Medium and heavy peptides have been correctly detected. The MultiplexResolver adds a dummy peptide feature of zero intensity at the light position and thereby completes the triplet.

(*) Note that the MultiplexResolver tool takes only a single (the first) peptide sequence annotation into account. By running IDConflictResolver first, it is assured that each multiplet has only one peptide sequence annotation, the best one. Multiplets without sequence annotation are passed to the optional out_conflicts output.

The command line parameters of this tool are:

    MultiplexResolver -- Completes peptide multiplets and resolves conflicts within them.

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

      MultiplexResolver <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>*            Peptide multiplets with assigned sequence information (valid formats: 'consensusXML'

                             )

      -in_blacklist <file>   Optional input containing spectral peaks blacklisted during feature detection. Neede

                             d for generation of dummy features. (valid formats: 'mzML')

      -out <file>*           Complete peptide multiplets. (valid formats: 'consensusXML')

      -out_conflicts <file>  Optional output containing peptide multiplets without ID annotation or with conflict

                             ing quant/ID information. (valid formats: 'consensusXML')

    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:

     - algorithm   Parameters for the algorithm.

     - labels      Isotopic labels that can be specified in section 'algorithm:labels'.

    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_MultiplexResolver.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+MultiplexResolver Completes peptide multiplets and resolves conflicts within them.
version 2.5.0-GIT-NOTFOUND-GIT-NOTFOUND Version of the tool that generated this parameters file.
++1 Instance '1' section for 'MultiplexResolver'
in Peptide multiplets with assigned sequence information input file*.consensusXML
in_blacklist Optional input containing spectral peaks blacklisted during feature detection. Needed for generation of dummy features.input file*.mzML
out Complete peptide multiplets.output file*.consensusXML
out_conflicts Optional output containing peptide multiplets without ID annotation or with conflicting quant/ID information.output file*.consensusXML
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
+++algorithm Parameters for the algorithm.
labels[][Lys8,Arg10] Labels used for labelling the samples. [...] specifies the labels for a single sample. For example
[][Lys8,Arg10] ... SILAC
[][Lys4,Arg6][Lys8,Arg10] ... triple-SILAC
[Dimethyl0][Dimethyl6] ... Dimethyl
[Dimethyl0][Dimethyl4][Dimethyl8] ... triple Dimethyl
[ICPL0][ICPL4][ICPL6][ICPL10] ... ICPL
missed_cleavages 0 Maximum number of missed cleavages due to incomplete digestion. (Only relevant if enzymatic cutting site coincides with labelling site. For example, Arg/Lys in the case of trypsin digestion and SILAC labelling.)0:∞
mass_tolerance 0.1 Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern.
mz_tolerance 10 m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted.
rt_tolerance 5 Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted.
+++labels Isotopic labels that can be specified in section 'algorithm:labels'.
Arg6 6.0201290268 Label:13C(6) | C(-6) 13C(6) | unimod #188 0.0:∞
Arg10 10.008268599999999 Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #267 0.0:∞
Lys4 4.0251069836 Label:2H(4) | H(-4) 2H(4) | unimod #481 0.0:∞
Lys6 6.0201290268 Label:13C(6) | C(-6) 13C(6) | unimod #188 0.0:∞
Lys8 8.0141988132 Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #259 0.0:∞
Leu3 3.01883 Label:2H(3) | H(-3) 2H(3) | unimod #262 0.0:∞
Dimethyl0 28.031300000000002 Dimethyl | H(4) C(2) | unimod #36 0.0:∞
Dimethyl4 32.056407 Dimethyl:2H(4) | 2H(4) C(2) | unimod #199 0.0:∞
Dimethyl6 34.063116999999998 Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #510 0.0:∞
Dimethyl8 36.075670000000002 Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #330 0.0:∞
ICPL0 105.021463999999995 ICPL | H(3) C(6) N O | unimod #365 0.0:∞
ICPL4 109.046571 ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #687 0.0:∞
ICPL6 111.041593000000006 ICPL:13C(6) | H(3) 13C(6) N O | unimod #364 0.0:∞
ICPL10 115.066699999999997 ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #866 0.0:∞