Lipid Peak Integration Boundaries

Lipid Peak Integration Boundaries dpeake  2021-02-17

Hi everyone,

I’m investigating using Skyline for integrating lipid annotation and QA/QC.
I have been very impressed with Skyline’s ease-of-use for quantitation.

I have several questions regarding adjusting integration parameters, in particular, the integration window that is displayed. When integrating a batch of lipids, some windows for the same species are displayed in a wider window than others. This window appears to change when the program sets different peak boundaries. This results in missed areas or integration of the another isomer, the largest peak in the window [see attached].

I would prefer to set a single integration window and peak boundary for all samples for a given lipid, thereby reducing the need for manual intervention.
After looking through this forum, I can't say that I have found any method that works. Adjusting the peak boundaries and "Apply to All" does not work.
Can anyone suggest a workaround other than manually changing peak boundaries one file at a time?


Nick Shulman responded:  2021-02-17
One thing that might work is creating a peak boundaries .csv file, and then doing "File > Import > Peak Boundaries".

Each row of that .csv file specifies the peak boundaries for a single molecule in a single file. So, if you wanted to set the peak boundaries in all of the files to the same values, you would probably use Microsoft Excel to merge a list of M files with a list of N molecules, and produce a .csv file with M times N rows in it.

It is a little confusing to get "Import Peak Boundaries" to work with small molecules. One thing is that you need to put the name of the Molecule in the column "Peptide Modified Sequence". Once you get past that trick, it might work pretty well. You can find more information about Import Peak Boundaries and small molecules towards the end of this support request:

Can you send us one of your Skyline documents? We might be able to come up with a good idea if we see it.
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
dpeake responded:  2021-02-17
Hi Nick,

I have uploaded the file as well as the peak boundaries csv that I created.
Hope this gives you a better picture of what is going on.