Slow import of Agilent MRM data into skyline vincentroyrichard  2022-08-19 08:09


We're having a recent problem where the import of MRM data specifically from our Agilent 6495 system seems to be slower than normal. Specifically data import quickly reaches 99% then hangs for about 15-20 seconds per data file before completing the import. I'm running Skyline Daily on a Windows 10 workstation. Import speeds for equivalent data generated with a Sciex QTrap 6500 is normal. Any assistance would be greatly appreciated.

Thanks very much,

Nick Shulman responded:  2022-08-19 08:22
Can you send us your Skyline document and one or more of your Agilent raw file folders?

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.
You should also zip up one or more of your Agilent .d folders.

If those zip files are less than 50MB you can attach them to this support request.
You can upload larger files here:

vincentroyrichard responded:  2022-08-19 08:56
Hi Nick,

Sure thing, please find the skyline document and some of the Agilent raw file folders attached.
Nick Shulman responded:  2022-08-19 09:54
Thank you for sending those files.

When Skyline imports SRM chromatograms, Skyline performs peak finding on all of the chromatograms regardless of whether the chromatogram matches any molecule in your document.
It looks like most of the time is being spent on trying to do peak finding on the Total Ion Current chromatogram. This is a waste of time for Skyline to be doing because the TIC chromatogram could never possibly match anything in your document.
The amount of time which it takes to do peak finding in a particular chromatogram is approximately proportional to the total length of the chromatogram times the number of points across the tallest peak. That is, Skyline first finds the tallest peak in the chromatogram, figures out how wide it is, and then that width is used to decide how wide of a filter to move along the chromatogram performing operations like smoothing.
Your TIC chromatograms have about 80000 points in them, and the tallest peak is about 2000 points wide.

I don't think anything has changed in Skyline in this area in a very long time, so if things seem slower than it used to be, I wonder if the TIC chromatogram in your files might be longer than it used to be, or the peaks are broader.

Thanks for sending use these files. I will see whether we can fix things in a future version of Skyline so that it never bothers trying to do peak finding on the TIC chromatogram.
-- Nick