Displaying peptide mod in left target sequences

Displaying peptide mod in left target sequences Erik de Graaf  2019-06-17

Hi all,

Currently I'm using skyline to quantify glycopeptides. However considering there are many glycan versions I end up with a big list of identical peptide sequences and it is hard to quickly see what glycan is on them (see attachment). Same goes for the peptide comparison plot that shows all the same sequence.

I now use note to write down the modifications, so when I hover over I can see the mod. However, this way I have to hover over all peptides to find the p.o.i.

Displaying the modified sequence in the list and graphs could greatly facilitate glycopeptide analysis.


Brendan MacLean responded:  2019-07-01
Good point. That was a decision made a long time ago when Skyline was a lot less widely used.

We have a menu item

View > Targets >
    By Name
    By Accession
    By Preferred Name
    By Gene

We could relatively easily add below it:

View > Peptides >
    By Sequence = PEPTIMER
    By Modified Sequence = PEPT[+80]IM[+16]ER
    By Modified Sequence Masses = PEPT[+79.966331]IM[+15.994915]ER
    By Modified Sequence Codes = PEPT[Pho]IM[Oxi]ER
    By Modified Sequence Full Names = PEPT[Phospho (ST)]IM[Oxidation (M)]ER
    By Modified Sequence Unimod Ids = PEPT(unimod:21)IM(unimod:35)ER

Skyline can already calculate all of these for display in reports. So, it shouldn't be that hard to show them in the Targets view based on a setting.

Brendan MacLean responded:  2019-07-01
Hopefully, we can get this implemented during the next release cycle: