It seems that msgf2pin does not use all of the PSMs as input. See for example the search 14956 from Robin and Mahshid, which crashed since extremely few were found. Investigate!
Maybe there is a cutoff value somewhere, in case of bad scores. It also does not consider multiple-sequence-match PSMs (with identical score, so same rank) it seems (although that can be fixed with a param).
It seems that msgf2pin does not use all of the PSMs as input. See for example the search 14956 from Robin and Mahshid, which crashed since extremely few were found. Investigate!
Maybe there is a cutoff value somewhere, in case of bad scores. It also does not consider multiple-sequence-match PSMs (with identical score, so same rank) it seems (although that can be fixed with a param).