Missing DIA acquisition

Missing DIA acquisition guilherme pauperiolanfredi  2024-04-11 00:08

I’m having issues regarding the DIA acquisition on TimsTOF Pro, for some of my runs.

The chromatography of all runs are comparable and I can see it during the run, but when opening it on Skyline the acquisition is not there, not even noise.

In this screenshot, two runs are shown where I have complete signal acquisition and two others that only have the first few minutes and then there is no signal, besides having complete chromatography on the vendor software.

Any idea?

Thanks in advance.

Nick Shulman responded:  2024-04-11 00:20
If you have a completely flat chromatogram with no signal, the problem might be that the signal that is there is outside of the m/z window that Skyline is summing across to extract chromatogram intensities.

If you click on a point along the chromatogram Skyline will bring up a window which shows you the spectrum that contributed to that point. Skyline will highlight the m/z window around the transition m/z which will show you what Skyline was summing across to extract the intensity.

The width of that m/z extraction window is controlled by the Resolution or Mass Accuracy specified at "Settings > Transition Settings > Full Scan" (it's called "mass accuracy" if the data is centroided and it's called "resolution" if not centroided.

If you would like you could send me your Skyline document and one or more 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.
The Share Document dialog also gives you the option to include your mass spec result files or you can zip them up separately and send them to us.

Files which are less than 50MB can be attached to these support requests. You can always upload larger files here:
-- Nick