I see the modification N[115], but not the color coding and also the calculation at the bottom of the page for # NxS/T peptides vs total # peptides is empty. I find this to be very useful when calculating specificity of our capturing method. If i know it is a bug, then I'll wait for a fix. Just wanted to make sure I wasn't supposed to be clicking any more buttons to get it to show up.
Thanks! Rebekah On Wed, Feb 29, 2012 at 9:46 AM, dshteynb...@systemsbiology.org < dshteynb...@systemsbiology.org> wrote: > Hello Ruby, > > I believe this problem is only with the ProteinProphet viewer not the > modelling. Someone else had reported this problem also but it has not been > fixed in this release. The problem is in the coloring off the motif only. > You should still see the motif in the peptides you identify. > > -David > > Sent from my Android Device > > > ----- Reply message ----- > From: "Ruby" <rubycell7...@gmail.com> > To: "spctools-discuss" <spctools-discuss@googlegroups.com> > Subject: [spctools-discuss] GLYC not working in 4.5.2? > Date: Wed, Feb 29, 2012 6:51 am > > > I have been using the GLYC command in TPP 4.4.0 for more than a year > with no problem. I recently upgraded to TPP 4.5.2 and can't seem to > get the GLYC command to work for ProteinProphet. I have the "N- > glycosylation data (color NXS/T)" option checked in petunia when doing > ProteinProphet processing, and in the ProteinProphet header the "NxS/ > T" box is checked. However, I do NOT see any pink highlighted N[115] > in the peptides like I used to see nor does it calculate the # of > glycopeptides at the bottom of the page - though most of my peptides > do contain this modification. I am selecting the option to use the > "Use N-glyc motif information" when I do the peptideprophet. > > Is there something else I"m supposed to be doing to get this to work > in the new update of TPP? > > Thanks > Ruby > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > For more options, visit this group at > http://groups.google.com/group/spctools-discuss?hl=en. > -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
