OpenMS
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/doxygen/release/3.2.0/html/TOPP_MultiplexResolver.html
Version: 3.2.0 Nov 26 2024, 13:16:38, Revision: 962e60f
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:
  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 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)

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/doxygen/release/3.2.0/html/TOPP_MultiplexResolver.html

INI file documentation of this tool:

Legend:
required parameter
advanced parameter
+MultiplexResolverCompletes peptide multiplets and resolves conflicts within them.
version3.2.0 Version of the tool that generated this parameters file.
++1Instance '1' section for 'MultiplexResolver'
in Peptide multiplets with assigned sequence informationinput 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)
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
+++algorithmParameters 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_cleavages0 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_tolerance0.1 Mass tolerance in Da for matching the mass shifts in the detected peptide multiplet to the theoretical mass shift pattern.
mz_tolerance10 m/z tolerance in ppm for checking if dummy feature vicinity was blacklisted.
rt_tolerance5 Retention time tolerance in seconds for checking if dummy feature vicinity was blacklisted.
+++labelsIsotopic labels that can be specified in section 'algorithm:labels'.
Arg66.0201290268 Label:13C(6) | C(-6) 13C(6) | unimod #1880.0:∞
Arg1010.008268599999999 Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #2670.0:∞
Lys44.0251069836 Label:2H(4) | H(-4) 2H(4) | unimod #4810.0:∞
Lys66.0201290268 Label:13C(6) | C(-6) 13C(6) | unimod #1880.0:∞
Lys88.0141988132 Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #2590.0:∞
Leu33.01883 Label:2H(3) | H(-3) 2H(3) | unimod #2620.0:∞
Dimethyl028.031300000000002 Dimethyl | H(4) C(2) | unimod #360.0:∞
Dimethyl432.056407 Dimethyl:2H(4) | 2H(4) C(2) | unimod #1990.0:∞
Dimethyl634.063116999999998 Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #5100.0:∞
Dimethyl836.075670000000002 Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #3300.0:∞
ICPL0105.021463999999995 ICPL | H(3) C(6) N O | unimod #3650.0:∞
ICPL4109.046571 ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #6870.0:∞
ICPL6111.041593000000006 ICPL:13C(6) | H(3) 13C(6) N O | unimod #3640.0:∞
ICPL10115.066699999999997 ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #8660.0:∞