Broad mass range for peak extraction

Broad mass range for peak extraction harald schoeny  2020-09-18

Dear Skyline Team,

I have lipid data measured on an HILIC- Orbitrap QExactive HF with an all ion fragmentation (AIF) approach. I figured it out to extract single masses with the help of the forum but I would like to extract a broader mass range (m/z 530-650 ) withing one peak. It should be the sum of all lipid species within one lipid class. Unfortunately, I couldn't find a way to do that in Skyline. I have tried to set the MS/MS filtering to Isolation scheme/Use results data isolation targets/ Isolation width/fixed/120 mz but nothing really happened. Is there another workaround for that?

Thank you in advance.
Best, Harald

Nick Shulman responded:  2020-09-18
I do not understand your question. Can you send us a picture of what you are asking about?

If you would like, you can send us your Skyline document and one of your raw files.

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.

Files that are less than 50MB can be attached to this support request. You can upload larger files here:

-- Nick
harald schoeny responded:  2020-09-21
Sorry for not being clear.

I have attached two pictures from Excalibur because I wasn't able to do it in Skyline yet.
The first one is a zoomed in mass spectrum. You can see several peaks and I would like to extract a chromatogram now, which includes masses over a whole mass range (530-650 m/z) and not just a single mass with a certain precision.

The second picture shows the desired chromatogram and a classical TIC.

I wasn't able to extract the same in Skyline because the optional columns for a transition list always include a specific formula or m/z value. Where can I either put in a mass range instead of a single m/z value or can I define the mass precision and say its +/- 60 Da?
Also, as it's All Ion Fragmentation, everything is MS2 and not MS1 but at least for single masses I have figured that out in Skyline.

I hope its better now. Thank you very much.
Nick Shulman responded:  2020-09-28
Sorry for the slow reply.

You can control the width of the m/z channel over which Skyline sums when extracting chromatograms by changing the "Resolving Power" at:
Settings > Transition Settings > Full Scan

Unfortunately, it appears that "1000" is the lowest value that Skyline will accept for Resolving Power. This would correspond to a channel width of approximately 1/1000th of the m/z of the product ion, which is nowhere near what you are looking for. It looks like you would like Skyline to sum across a channel width that is more than 100 units wide.

I do not believe that there is any way to get Skyline to do something like this.
-- Nick
Brendan MacLean responded:  2020-09-29
Yeah. Even if you were to choose QIT which would allow you to enter a resolution in m/z units, the maximum appears to be 2.0 right now, and you appear to be looking to achieve 120 m/z as your range.