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 ?
We had a similar report a few weeks ago. Now, I investigated a bit and I think this little bug was introduced recently when adding the option for processing in chunks.
For now, can you configure the node, go to the OutputTypes tab and deactivate the candidates_out output? If this (more or less debug-type output) is inactive, it should continue with the filtered data only which if I saw correctly, does not have the problem and is perfectly fine for running the tool.
Making sure that there is only one chunk might be another option if you need this output or if it does not work.
thank you so much for your prompt reply !! Worked like a breeze ! Let me express at this point that openms is one of the best, if not the best proteomics toolset available. Well done !! Extremely well done !!