I have been having trouble reading mzIdentML files from Comet (v. 2021010). It seems there are some unresolved references in the file that are causing pyteomics' MzIdentML class to read the file super inefficiently. Sadly, this is not something I can fix here, but I want to make note of it. When using Comet, the pepXML output may be best as an input to pyAscore. Or, better yet, just use the TXT file output from Mokapot or Percolator.
I have been having trouble reading mzIdentML files from Comet (v. 2021010). It seems there are some unresolved references in the file that are causing pyteomics' MzIdentML class to read the file super inefficiently. Sadly, this is not something I can fix here, but I want to make note of it. When using Comet, the pepXML output may be best as an input to pyAscore. Or, better yet, just use the TXT file output from Mokapot or Percolator.