OpenMS
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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:

INI file documentation of this tool: