Dear Crux team,
I am using crux percolator to calculate spectrum, peptide, and protein level q-values. The output format I use was mzid file created by crux percolator.
I noticed that the DBS index number in the beginning and end of mzid file does not really match(?) therefore, ProteinAmbiguityGroup can not be mapped to correct protein name (database sequence entry; DBS).
Please see the example below for more details . The mzid used in the example also attached in post.
Could you give suggestion on how to extract protein level q-value using mzid?
This is the ProteinAmbiguityGroup in the mzid file.
This is the beginning of SequenceCollection. The DBS index starts from 1: DBS_1. There is no DBS_0 in the sequence collection
I mapped the PAG_ID with SequenceCollection by using DBS_ID to get the protein accession for each PAG.
There are 8,254 ProteinAmbiguityGroup and 6,775 of them can not be mapped to any of DBS index.
For example DBS_0 just shown above and DBS_34 and DBS_51 below