Julian Uszkoreit

Hej @jpfeuffer , Sure, the symlink works for know. But would be great to have it shipped in working condition again, looking forward to it. After googling a bit more,...

Could you please provide me with files, where this happens?

Hej @cctsou , PIA currently supports using files created by Tide, see e.g. https://github.com/mpc-bioinformatics/pia/blob/master/src/test/resources/tide-search-cut.txt If you can bring your CSV in this format, you should be able to parse them...

Hej @cctsou , Could you solve your problem? Best, Julian

Hej @mcburke-msdc , The tide and CSV parsing seems to need an update, but do you actually still have this issue (apologies for the very late answer).

There is a new filter named "PSM_SET_CONTAINS_SCORE_FILTER" now (see PR #123). This works like a normal literal filter and only PSM sets containing the given score are passed on. If...

No, the second task is still missing ;)

Hej Marco, Actually, PIA should work with DIA data as well, as long as you only want to look at the identification values. I never tried it with OpenSwath, though...

Right, PIA can only create the protein grouping on the given peptide identifications. This information can be passed on to protein quantifiers, though. It works currently nice together with OpenMS,...

I am referring to the OpenMS tool/module ProteinQuantifier (http://ftp.mi.fu-berlin.de/pub/OpenMS/release-documentation/html/TOPP_ProteinQuantifier.html). This takes the grouping of PIA (peptides assigned to protein groups) and uses it for the calculation of protein quantifications.