MatthewThe

The q-values should be valid, as they are calculated on the PSM list after applying TDC.

This might be possible by setting `CPACK_RPM_PACKAGE_RELOCATABLE` to `TRUE` and `CPACK_SET_DESTDIR` to `FALSE` in CPack.txt.

Percolator now has a standalone zip file for Linux, e.g. [percolator-noxml.zip](https://github.com/percolator/percolator/releases/download/rel-3-06/percolator-noxml.zip) This should work without requiring sudo privilege but might fail in case some system libraries are not available. This...

This is probably related to #89. It could be that MS-GF+ changed from `cvRef="UNIMOD"` to `cvRef="PSI-MS"` in newer versions. Could you share a (small) example mzid that produces this problem?...

The problem was indeed what I expected. In earlier versions the cvref attribute was UNIMOD, and now it is PSI-MS (which indeed makes more sense): ``` ``` I will fix...

These warnings are quite normal. If I remember correctly, these are from uninformative PSMs anyway, so no need to be concerned.

Ah, sorry, this is indeed not fixed yet... A quick workaround would be to replace ``` ``` with ``` ``` in your mzid file.

Apologies for the very late reply. This sounds like a problem in the format of the mzid file after MzidMerger. Did you manage to solve the problem already? If not,...