Xin, You shouldn't have to run separate searches. Your attached images where the mzXML file name is XW3127C3OUT.mzXML implies that there's an error in the file name encoding somewhere. Presumably the file should be XW3127C3_090129.mzXML.
Feel free to send me your pep.xml file and I'll take a look to see if I can see what's going wrong. - Jimmy Xin Wei wrote: > Hi Oded, > > Let me see if I understand you. What I did is I searched Sequest using > +28Da on K and n-terminus as fixed modification and +4Da on these two > sites as variable modification. So my Sequest .OUT files contains the > information of both versions of labeling. Now are you asking me to run > the Sequest again, but using +28 and +32 individually in two searches, > and generate different .OUT files? > > Actually I've tried this approach before using Sequest only and it > didn't work well with lower number of identifications and maybe higher > false positives. I've never used this approach on TPP EXPRESS. > > Other than this suggestion, could you think of any reason that this > problem occurs? I am wondering if there is another way to get over > this. > > Thank you very much for your advice! > > Xin > > On Apr 22, 2:08 pm, Oded <oded.kleif...@gmail.com> wrote: >> Hi Xin, >> Try this: >> Make 2 copies of your mzXML/mzXL file (profile is better in my hands). >> Run 2 separate searches one for fixed light modification (N-term and >> K) and one for the fixed heavy modification, using one of mzXML for >> the light and the other for the heavy. >> Convert each of the search outputs to pepXML >> Run peptide prophet on both pepXML and set in the Xpress section >> "Change XPRESS residue mass difference:" to the mass difference >> between the heavy and light (i.e. ~4) for K and for N-term (called >> "n") >> Good luck, >> Oded >> >> On Apr 21, 9:30 pm, Xin Wei <catroy...@gmail.com> wrote: >> >>> Dear all, >>> I just had a problem with the XPRESS quantitation. All the ratios were >>> -1.0 and when I clicked on the ratio, I couldn't see any scans or >>> extracted ion chromatogram. >>> I used formaldehyde labeling on lysine (K) and N-terminus, so it's +28 >>> Da on light label and +32 Da on heavy labels, with 4Da difference. >>> I have uploaded two screen captures of what I described in the Files >>> named "XIC" and "EXPRESS". Has anyone had similar problems before? >>> Your help is greatly appreciated! >>> Xin > > --~--~---------~--~----~------------~-------~--~----~ 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 -~----------~----~----~----~------~----~------~--~---
