when trying to apply Hendrik Weissers workflow from this paper:
J Proteome Res. 2017 Aug 4; 16(8): 2964–2974. PMCID: PMC5547443 Targeted Feature Detection for Data-Dependent Shotgun Proteomics
in FFId mode with external identifications but without machine learning, the FeatureFinderIdentification Node throws following error:
unable to read file (<filename) ProteinIdentifications are not unique, which leads to loss of unique peptide assignment. Duplicated Protein-Id is: unique_run_identifier.
The input are MSGFPlus mzId files, unmatched peptides removed, otherwise unfiltered. Any idea what I am doing wrong here ?