Hi Everyone, I am trying to detect false positive rates in my TPP runs. I want to make sure that my probability result measures are actually correct. I have read some papers describing high levels of false positives and using decoy sets to correct for these errors.
I originally downloaded Mayu, made a fasta file with the appended decoy set (appending rev to the beginning of decoy sequences). I ran this through SEQUEST (inside of TPP). I tried to run Mayu (through command line) on the pepxml results of TPP. But I kept getting an error where it said the input file has no data. I think it was not parsing the pep.xml file correctly. Then i noticed that TPP has an option for running Peptide Prophet with a decoy correction. I took my output and ran peptide prophet with the decoy correction enabled. I noticed the output has decreased probability scores for the lower probability scores when this correction was enabled. MY QUESTION: What is the "Use decoy hits to pin down the negative distribution" checkbox actually doing? Is it using the Mayu software? And if it is not using Mayu, is it as accurate at reducing false positives as Mayu? Is there any change in the output other than probability score? Is there anything I need to know or do differently to correctly filter out false positives? I would like to have increased confidence in my peptide matches because our group is trying to match new sequences that you would not normally find in the mass spec data. Thanks for all the help, Kris --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
