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lehtiolab / ddamsproteomics

A Nextflow MS DDA proteomics pipeline
MIT License
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msgf2pin does not use not all PSMs in a run #27

Closed glormph closed 7 months ago

glormph commented 11 months ago

It seems that msgf2pin does not use all of the PSMs as input. See for example the search 14956 from Robin and Mahshid, which crashed since extremely few were found. Investigate!

Maybe there is a cutoff value somewhere, in case of bad scores. It also does not consider multiple-sequence-match PSMs (with identical score, so same rank) it seems (although that can be fixed with a param).

glormph commented 11 months ago

That search contained utter crap PSMs, so investigate somewhere else please, if we need to add any params.