Protein abundance issue

Protein abundance issue francescodemetrio lofaro  2021-01-13

Hello there,

I'm a new user of Skyline. I imported my DDA search from Mascot and I'm able to quantify proteins in two different conditions using MSstats. However, using this tool i can't quantify protein inside samples, but I obtaine only log of fold chande between conditions. So, is it possible to obtain protein quantification for each sample using MSstat integreted in Skyline?

Furthermore, i tried to quantify protein using protein abundance report integrated in Skyline. However, there are different missing values (#NA) for proteins that show peptide intensity in Skyline interface. How can resolve this issue?
I hope to find a solution to quantify in MS1 my samples thanks to your help.


Nick Shulman responded:  2021-01-13
Skyline will report the Protein Abundance as #N/A if any of the peptides in that protein have a transition which is missing a peak area.
One reason that a transition would be missing a value would be if you right-clicked on a peak and chose "remove peak".

You will probably be able to figure out which transition has a missing value in that Replicate.

If you cannot figure out what is going on, you can send us your Skyline document.
In Skyline, you can use the menu item:
File > Share
to create a .zip file containing your Skyline document and supporting files including extracted chromatograms.

If that .zip file is less than 50MB you can attach it to this support request. Otherwise, you can upload it here:

-- Nick