Different dotp value in peak area view and target window

Different dotp value in peak area view and target window meharunnissakohli  2021-08-13

Dear Support Team,
I was using Skyline for analyzing an MRM based data and also using a spectral library. During analysis, for some of the peptides, I noticed that the dotp value shown in 'peak area view' and that in 'target window' are different. However, for most of the other peptides, it is same at both the places.

Could you please help me understand the problem. Looking forward to hearing from you.
Attached here is the screenshot for the same.


Nick Shulman responded:  2021-08-13
Can you 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
Brendan MacLean responded:  2021-08-13
Hi Mehar,
Can you try turning on Settings > Integrate All? When I look at your peak areas plot it looks to me like a fair number of transitions are not represented in the empirical data. I am still a little surprised that the targets view and the peak areas plot aren't showing the same dotp, but it may be related to not having "Integrate All" checked.

Let me know what you see.

Thanks for posting to the Skyline support board.