|neutral loss of glycopeptides||kpan||2017-05-04|
We are now working on targeted glycoproteomics, where the glycopeptides are measured using DIA and the resulting raw files were processed by Skyline. Unfortunately, Skyline of it's current version is not quite convenient for glycoproteomic analysis. Under beam-type CID of glycopeptides, the "glycan Y ions" (or the intact peptide core plus couple of glycan moieties, see attached slide#1) usually dominate the MS/MS spectra at the m/z region >600 Th and are good targets for detection. We attempted to include the glycan Y ions in our target list in Skyline by editing neutral loss table of N-glycosylations in the modification page of peptide settings (slide #2 left). We could indeed then find the target ion in our target list (slide #2 right). The problem is that somehow Skyline limits such neutral loss ions to be bearing the same number of charges as it's precursor does, 3+ in the shown case. But actually it is more often to see these glycan Y ions with 1+ or 2+.
So here is my question, is it possible to freely ask skyline to monitor ions with the charge state that is defined by user? Or even better if one could simply define a modification as a kind of N-glycosylation and the software would automatically include corresponding glycan Y ions as targets.
Thank you very much.
I appreciate your help and am looking forward to hearing from you.