psmfeatureextractor failes on merged idXML files

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Dear All,

I am trying to replicated Hendrik Weissers MHC Workflow, with a few changes.

Basically the workflow is as follows:

  1. Detection with MSGFPlus, annotation with PeptideIndexer
  2. Alignment mit MapAlignerIdentification followed by MapRTTTransformer
  3. Merging of the aligned idXML files with ID merger

After this step, I would like to apply Percolator to the merged idXML file (as in the MHC Workflow), however, PSM FeatureExtractor throws following error:

error: Unexpected internal error (the element No accession found in run for PSM . Please contact the maintainer of this tool e.g. on GitHub as this should not happen." could not be found.

Any ideas what is going on here ?

thanks a lot,
best,
Thomas

2

Hi!

How did you configure IDMerger? Can you somehow send the configuration (non-advanced parameters should be enough)?
Unfortunately, it evolved over time and there are multiple modes to merge. The best way to merge for Percolator would probably be to enable the rather new “merge_proteins_add_psms” option.

3

Hi Julianus, thanks for the prompt reply. Worked like a charm. If you ever happen to be in Vienna, drop me a line. The first beer is on me.

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