-Ogp should work. On Thu, Jun 11, 2009 at 10:25 AM, Ruby<[email protected]> wrote: > > 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 >> >> > > >
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