MultiplexResolver

Completes peptide multiplets and resolves conflicts within them.

pot. predecessor tools	$\longrightarrow$ MultiplexResolver $\longrightarrow$	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.
Version: 2.3.0 Jan  9 2018, 17:46:23, Revision: 38ae115

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'
                         )
  -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.
Have a look at the OpenMS documentation for more information.

INI file documentation of this tool:

Legend:

required parameter

advanced parameter

+MultiplexResolverCompletes peptide multiplets and resolves conflicts within them.

version2.3.0 Version of the tool that generated this parameters file.

++1Instance '1' section for 'MultiplexResolver'

in Peptide multiplets with assigned sequence informationinput file*.consensusXML

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 Overwrite tool specific checks.true,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 detected to the theoretical mass shifts.

+++labelsIsotopic labels that can be specified in section 'algorithm:labels'.

Arg66.0201290268 Label:13C(6) | C(-6) 13C(6) | unimod #1880:∞

Arg1010.0082686 Label:13C(6)15N(4) | C(-6) 13C(6) N(-4) 15N(4) | unimod #2670:∞

Lys44.0251069836 Label:2H(4) | H(-4) 2H(4) | unimod #4810:∞

Lys66.0201290268 Label:13C(6) | C(-6) 13C(6) | unimod #1880:∞

Lys88.0141988132 Label:13C(6)15N(2) | C(-6) 13C(6) N(-2) 15N(2) | unimod #2590:∞

Leu33.01883 Label:2H(3) | H(-3) 2H(3) | unimod #2620:∞

Dimethyl028.0313 Dimethyl | H(4) C(2) | unimod #360:∞

Dimethyl432.056407 Dimethyl:2H(4) | 2H(4) C(2) | unimod #1990:∞

Dimethyl634.063117 Dimethyl:2H(4)13C(2) | 2H(4) 13C(2) | unimod #5100:∞

Dimethyl836.07567 Dimethyl:2H(6)13C(2) | H(-2) 2H(6) 13C(2) | unimod #3300:∞

ICPL0105.021464 ICPL | H(3) C(6) N O | unimod #3650:∞

ICPL4109.046571 ICPL:2H(4) | H(-1) 2H(4) C(6) N O | unimod #6870:∞

ICPL6111.041593 ICPL:13C(6) | H(3) 13C(6) N O | unimod #3640:∞

ICPL10115.0667 ICPL:13C(6)2H(4) | H(-1) 2H(4) 13C(6) N O | unimod #8660:∞