Hi all, I have searched LTQ-FT data against a decoy database using X!Tandem/k- score. As for the xinteract command, I enable the accurate mass binning and use the decoy hits to pin down the negative distribution. My question is regarding the non-parametric model option. By enabling it, I usually get more peptide identifications. But the truth is that I don't quite understand what this non-parametric modeling is. I did read several posters and papers from Nesvizhskii, Shteynberg, among others, but I couldn't find a more detailed answer. Can anyone help a non-statistician?!?!?!
One more question, I understand that most people use a 'relaxed' precursor tolerance, say 2 Daltons, to search non-decoy database with XTandem, and then use Peptide Prophet with accurate mass binning. What about searches against decoy databases?? Do 'relaxed' tolerance work better than more strict tolerances?? I have tried 2Da against 20 ppm decoy searches both using ACC MASS BIN and haven't seen much difference. Has anyone have a different experience?? I'd appreciate any advice. Thanks, Alex --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
