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OpenSwathDecoyGenerator

Generates decoys according to different models for a specific TraML

potential predecessor tools $ \longrightarrow $ OpenSwathDecoyGenerator $ \longrightarrow $ potential successor tools
FileFilter OpenSwathAnalyzer

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.

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 and shuffles the fragment ion intensities accordingly, however for this to work the fragment ions need to be matched to annotated before.

The command line parameters of this tool are:

The algorithm parameters for the Analyzer filter are:


OpenMS / TOPP release 2.0.0 Documentation generated on Fri Jan 15 2016 14:22:32 using doxygen 1.8.9.1