Hi David, The samples have been digested with a cocktail of enzymes, therefore non specific and no enzymatic rules. That's what I thought too that I would have to turn off NTT and NMC for these type of data. I run them by specifying "nonspecific" both for Out2XML or Mascot2XML as well as for xinteract -nE. But although I could see a lot of nice spectrum, most of them were not validated or discarded. Will try the NTT or NMC off. I just wanted to have some input about how someone should validate such type of dataset as usual one have some enzyme specificity.
Thanks David. Alex On Mar 26, 7:58 pm, David Shteynberg <[email protected]> wrote: > Hi Alex, > > Is the search non-specific or there the correct peptides are not > expected to conform to any enzymatic rules? If it is the latter you > should disable the NTT and NMC models in the TPP, since correct > peptides are not any more likely to have certain ends than the > incorrect peptides. If it is the former then you should specify the > enzyme when you run InteractParser and that way the NTT and NMC info > will be recorded in the interact.pep.xml file despite the search being > nonspecific. Does that make sense? > > -David > > > > On Fri, Mar 26, 2010 at 6:12 AM, Alex <[email protected]> wrote: > > Hi All, > > > I'd like to have some opinions on how to validate a dataset with > > no_enzyme specificty using PeptideProphet ? > > > Until now it looks like it's difficult to get a model working. I > > converted to pepxml using -Enonspecific from Mascot or Sequest by it > > looks like the model has difficulty. I'm wondering who has experience > > with nonspecific samples and validation. Should I turn off some > > standard features like -OFNM ??? > > > Thanks for any help. > > > 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 > > athttp://groups.google.com/group/spctools-discuss?hl=en.- Hide quoted text - > > - Show quoted text - -- 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.
