I got 5 search engines running for PSM matches, and also the Fido adapter. The data for Fido are prepared by Search Engine -> PeptideIndexer -> IDPosteriorProbability -> Fido adapter.
I also tried the sequence of Workflow https://cibi.uni-konstanz.de/socialworkflows/workflows/OpenMS:MHCLigandomics_new
However, the Percolator Adapter does not accept these data.
What are the modules/ parameters needed to prepare the data for Percolator?
KNIME 3.5.3 and OpenMS 2.3
I might be late, but I’ve been using the PercolatorAdapter sucessfully using the following workflow:
Search Engine -> PeptideIndexer -> PSMFeatureExtractor -> PercolatorAdapter -> IDFilter
Hope it helps !