Thanks!1 So just to clarify, I can use -Ogp to do the glyco model + run protein prophet afterwards...or should it be -Og -Op (separate)?
On Jun 11, 1:21 pm, David Shteynberg <[email protected]> wrote: > Hi Rebekah, > > Using -Og as an xinteract option will enable the use of the Glyco > model to modify the probabilities. If you are using xinteract you > should not have to run PeptideProphetParser separately, xinteract > will do it for you and enable all the correct options. > > -David > > On Thu, Jun 11, 2009 at 9:09 AM, Ruby<[email protected]> wrote: > > > I am a bit confused on the best manner in which to process data from > > an N-linked glyco capture experiment, analyzed via the orbitrap. I > > know how to 'highlight' those peptides with the NxS/T motif, but am > > hoping that there is also a way that the algorithms can somehow reward > > or otherwise consider the motif in the probability calculations as > > well. > > > What is the difference between the following options: > > 1) PeptideProphetParser interact.xml GLYC - which "uses peptide NxS/T > > motif in probability calculation" > > 2) -Og - which "uses N-glyc motif information in PeptideProphet" > > > It seems like either option would affect the data at the > > peptideprophet level, and 'reward' those peptides that contain the > > motif. Correct? > > > When I try option #1 by typing in "PeptideProphetParser interact.xml > > GLYC", I get an error: "cannot parse input file PeptideProphetParser" > > Help!!??? > > > Thanks! > > Rebekah > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
