One peptide, two heavy labels?

One peptide, two heavy labels? ztflaten  2019-12-13

Hey Skyline Forum,

I have a peptide with two labels. One is a N15 labelled full protein that is added to monitor digestion, the other has a single amino acid label. They share the same light peptide, but I've had to "duplicate" it to have both modifications present in Skyline. Is there a better way to do this? The issue ends up being if I change the integration window for one, it ends up having a different light peak area than the other.

I've attached a screenshot of what this looks like in my work space.



Brendan MacLean responded:  2019-12-13

There is a better way to do it. Just add a 3rd isotope label type. Here are some documents that do this: Public/2015/Schilling - main_Study_9/Study_9.2_CalCurves/begin.view

It is also explained in the webinar on modifications in Skyline (see Isotope Labeling in the table of contents):

Nick Shulman responded:  2019-12-13
Skyline lets you have more than one type of "heavy" peptide.
To do this, go to:
Settings > Peptide Settings > Modifications
and in the "Isotope Label Type" dropdown click "edit list".

You then need to decide what to name your different "heavy" types and list them on separate lines in the big textbox that comes up. For instance:
heavy 15N

After you have done that you will be able to right-click on peptides in the Targets tree and choose "Modify..." and you will be able to specify separately how the "Isotope heavy" and "Isotope heavy 15N" forms should be modified.

In the Peptide Settings Modifications dialog you can also choose which Isotope Modifications should be automatically applied for each label type.
-- Nick
ztflaten responded:  2019-12-13
Thanks for the help and quick response!