|Problems import spectra for laballed peptides from a Sequest search||marten sundberg||2015-03-27|
I experienced a new difficulty yesterday when I wanted to import a Sequest search for Q Exactive runs (PRM)with both light and heavy peptides. I have isotopically labelled peptides that I run in a standard curve with different concentrations. I set the modifications in Proteome discoverer to:
Dynamic Modification: Label:13C(6)15N(4) / +10.008 Da (R)
Dynamic Modification: Label:13C(6)15N(2) / +8.014 Da (K)
For the peptide GIVEEccFr I got hits for both the light and the heavy form as can be seen in the attached file. When I tried to import that .msf file to Skyline I was asked to specify which modifications that I wanted to include. Deamidated and Oxidation was ok but for the labelling Skyline suggested
As also can be seen in the attached file. Which is not what I have in the file. I have C terminal labelling of :
This means that no spectra from the labelled peptides will be included in the import and no spectra library will be created for those peptides. As you can see in the file the spectra library is the same both for the heavy and the light peptide. Could this be done in a different way so I also can import spectra for the heavy peptides?