Is it possible to set the min and max peptide mass?
Bo
@wenbostar
@courcelm , we don't have parameters to control the peptide mass but you could use "-minLength" and "-maxLength" to limit the peptides considered in the search.
Hello, I have run PepQuery but in psm_rank.txt file the column "confident" is missing
Bo
@wenbostar
@qudratbt_twitter , sorry for the late reply. I didn't check gitter frequently. If the column "confident" is missing in psm_rank.txt, it means all the PSMs in the file are not confident based on p-value or competitive filtering based on unrestricted post-translational modification searching.