Chromatogram information unavailable JUST for the Heavy Label

Chromatogram information unavailable JUST for the Heavy Label cvarcini  2024-01-30 11:41


I'm encountering an issue with my internal standard, a heavy label of one of my molecules, in Skyline. While I can see all the chromatograms, the one for the heavy label isn't processing properly. I've attempted this with both Skyline and Skyline Daily, experiencing the same issue on both platforms. I've uploaded two different transition lists, one with the heavy label having the same name as the molecule, and another with a different name. Unfortunately, neither has worked. I've verified the raw data, and I'm confident the peak is present.

How can I resolve this problem and successfully use Skyline to quantify samples using my internal standard?

Nick Shulman responded:  2024-01-30 12:07
The reason that you are not getting any chromatograms for that molecule with the precursor 400.3653 is that the chromatograms that in the .raw file have a Q1 value of 400.5.

You can control how closely the precursor m/z and Q1 values have to be for Skyline to consider them to be a match. The setting that controls this is "Method match tolerance m/z" at "Settings > Transition Settings > Instrument". The default value for this setting is 0.055, which is less than the difference between 400.3653 and 400.5, so there is no matching chromatogram for that particular precursor.

By the way, if you want to send someone your Skyline document, the easiest way to do that is with the "File > Share" menu item which creates a .zip file containing the Skyline document and all of the supporting files that you attached to this message.

-- Nick