Hi, I am using TPP version 4.2.1 on windows. My raw file is from Orbitrap. The process until peptide prophet works smoothly. I am searching with Mascot against a database that includes decoy entries and no enzyme. I use the following run options for peptide prophet: MINPROB=0.05 ACCMASS The peptide prophet command ends successfully, but in the result pepXML file all the peptides has a negative probability and when looking in the plotmodel it is written that "Estimated total number of correct peptide assignments in dataset: 0.0 ".
Do I use the correct run options? Should I choose other options? Thanks, Keren --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
