HI, running TPP 4.0 and 4.1 (gui and cmd) and having difficulty with high homology protein and MSMS data sets within peptide prophet. Upgrade from 4.0 to 4.1 did not solve the problem. I get an error message within xinteract as follows when parsing Mascot data sets:
WARNING: Mixture model quality test failed for charge (2+) Use xinteract option -OF (PeptideProphetParser option FORCEDISTR) to override. I've tried forcing as follows: xinteract -Nname-interact.pep.xml -p0.00 -l1 -x20 -OlNFp -I1 But I received the same error message. The result is that all (2+) peptides have a peptide prophet probability of -2 or 0. The Mascot scores are solid for these MSMS data. (3+) MSMS data is fine. Any ideas???? Thanks! --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
