Hi Rebekah, Since this is strictly a viewer issue, you may also just install the old viewer so you can take advantage of the motif coloring and stats while we come up with a fix. You can either copy the protxml2html.pl file from another machine that has the TPP (pre-4.5.1) installed into the tpp-bin directory, or we can give you one. Cheers, --Luis
On Wed, Feb 29, 2012 at 12:39 PM, Rebekah Dawson <[email protected]> wrote: > 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, [email protected] > <[email protected]> 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" <[email protected]> >> To: "spctools-discuss" <[email protected]> >> 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 [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. >> >> -- >> 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. > > > -- > 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. -- 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.
