PTM annotation

PTM annotation rajirathore3  2020-08-06

Hi Skyline Team

I am working on Glycation (a PTMs) of selected peptides of Albumin protein where I look for different types of glycation modifications of each peptide but when I add them in workflow it sums up the modifications shown in attachment. I have tried first with one of the representative peptide KVPQVSTPTLVEVSR where I specified 3 different glycation modifications on first lysine site. I added them separately in modification list and I was expecting it to be annotated separately but it has summed up two different lysine modifications and which does not meet my experimental workflow.
I want it to be annotated like K(58)VPQVSTPTLVEVSR and K(72)VPQVSTPTLVEVSR not K(130)VPQVSTPTLVEVSR. Please suggest me how this can be performed.


Nick Shulman responded:  2020-08-06
I think you should uncheck these modifications in "Settings > Peptide Settings > Modifications".
Modifications which are unchecked in that list are available in your Skyline document, but only get applied if you tell Skyline to apply them (by, for instance, right-clicking on the peptide in the Targets tree and choosing "Modify Peptide"). These are called "explicit modifications".

If you check the box next to the modification, then they become "implicit modifications", which means that Skyline applies these modifications

This webinar is very helpful in terms of explaining the difference between implicit, explicit and variable modifications:

-- Nick
rajirathore3 responded:  2020-08-06
Thank you Nick for the details.