dear list, i tried to run the combination of interactparser/refreshparser/peptideprophetparser instead of xinteract. however when i try to 'emulate' the xinteract parameter
-dDECOY_ -OAPdlIw with interactparser: -L7 -Etrypsin -C refreshparser: PREV_AA_LEN=1 NEXT_AA_LEN=1 peptideprophetparser: DECOY=DECOY_ ACCMASS NONPARAM DECOYPROBS LEAVE PI INSTRWARN MINPROB=0 i do get around 5% less identifications at the same cutoff (1% fdr) it would be great when one of the experts could tell me what i am doing wrong and how to fix it? many thanks in advance, andreas -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
