This KNIME workflow shows the very basics of peptide identification using OpenMS.

What it does:

It shows how to use a peptide search engine adapter (here: OMSSA) on multiple input files using the same database multiple times.

This workflow is part of the OpenMS tutorial and described in detail in the tutorial.

Preset parameter assumptions:

You have recorded MS/MS data in CID mode and medium resolution (comparable to an ion trap)

Important parameters:

OMSSAAdapter

database expects NCBI formatted FASTA files. The .psq filename should be given.
precursor_mass_tolerance choose according to your acquisition settings
fragment_mass_tolerance choose according to your acquisition settings