OpenMS
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OpenSwathDecoyGenerator

Generates decoys according to different models for a specific TraML.

potential predecessor tools → OpenSwathDecoyGenerator → potential successor tools
OpenSwathAssayGenerator OpenSwathAnalyzer
OpenSwathWorkflow

This module generates "decoy" transitions from a set of real or "target" transitions. The idea is to use the decoy transitions in a statistical scoring process to estimate the false hits in an SRM / SWATH experiment. The tool operates on TraML files, which can come from TargetedFileConverter or any other tool.

There are multiple methods to create the decoy transitions, the simplest ones are reverse and pseudo-reverse which reverse the sequence either completely or leaving the last (tryptic) AA untouched respectively.

Another decoy generation method is "shuffle" which uses an algorithm similar to the one described in Lam, Henry, et al. (2010). "Artificial decoy spectral libraries for false discovery rate estimation in spectral library searching in proteomics". Journal of Proteome Research 9, 605-610. It shuffles the amino acid sequence (excluding N-/C-terminal and K/R/P) and shuffles the fragment ion intensities accordingly. If the new sequence does not reach a threshold of identity within a set number of trials, a random amino acid (not N-/C-terminal or modified) is "mutated" to a random other amino acid.

The command line parameters of this tool are:

INI file documentation of this tool: