Sure Quant quantification issue with thermo tune version 3.5

Sure Quant quantification issue with thermo tune version 3.5 clemence balty  2021-11-09


We are currently facing some problems with an existing custom SureQuant method that we had developed with the previous version of the thermo Tune software(3.3). With the current version (3.5) we are unable to reproduce previous results (see attached ppt). Peaks are present in the raw data (analyze with freestyle), but absent or troncated in skyline. I used the same method of analysis.

Do you think there might be a compatibility issue with the new version of the thermo Tune software ?

Thank you,

clemence balty responded:  2021-11-09

The column has been changed between the two run, therefore the retention times will not be the same, but this should have no consequence with a SureQuant method

Nick Shulman responded:  2021-11-09
When you have the "Triggered chromatogram extraction" checkbox checked at "Settings > Transition Settings > Instrument", Skyline tries to detect the times along the chromatogram where any of your precursors were not having data collected for them.

The way that Skyline finds gaps in a chromatogram is to first figure out the median time between points along the chromatogram. After that median has been determined, any place along the chromatogram where the distance between two points is more than ten times that median is a gap.

After the gaps in the chromatograms have been found, those gaps are then applied to all of the precursors belonging to that molecule.
In the PowerPoint that you attached, the reason that chromatogram starts at around 38.0 minutes is probably that your light precursor did not have any matching MS2 spectra before that time.

If you send us your Skyline document and raw files I will probably be able to give you a more detailed explanation of why Skyline is doing what it is doing.

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 and your raw files are less than 50MB you can attach them to this support request.
You can upload larger files here:
-- Nick