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Schedueld SRM data analysis problem

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Schedueld SRM data analysis problem kallo gergo  2018-08-15 01:20
 

Dear Skyline team!

I have a problem with scheduled data analysis in Skyline and I would like to ask your advice. I am analyzing small molecules in scheduled SRM mode in an ABSciex 4000QTRAP instrument. My samples are derivatized and I monitor the end product of the reaction. After the CID I check the derivatization fragment so the Q3 is the same for all transitions. I am using stable isotope-labeled compounds and because of the different isotopic labels the m/z of several parent ions is the same. I can register the signal for all of my transitions but the problem comes when I want to analyse the data in skyline. For those molecules which have exactly the same transition but has different retention time I only see data for the first retention time window in skyline. In that case I cannot integrate those peaks which elute at another retention time. I tried to find some solutions in the options of the skyline but I cannot fix this problem.
Maybe I just missed something, could you please help me to fix this problem?

Yous sincerely,
Gergő Kalló
University of Debrecen
Department of Biochemistry and Molecular Biology
Hungary
 
 
Nick Shulman responded:  2018-08-15 02:45
If you want to tell Skyline what time to expect the molecule at, you can set the Explicit Retention Time.
You can set the Explicit Retention Time in the Document Grid. The Explicit Retention Time column should be visible if you change the View on the Document Grid to "Peptides".

Skyline uses the Explicit Retention Time value in order to figure out which chromatograms in a SRM result file belong with which molecule. If the time range of the chromatogram does not overlap with the specified Explicit Retention Time, then Skyline will try to choose a different chromatogram.

After you change the Explicit Retention Time, you will probably have to reimport the results (Edit > Manage Results > Reimport) in order to see the effect of the change.

If setting the Explicit Retention Time does not work, then Skyline might be getting confused in terms of figuring out which chromatograms go with each other, and what their time ranges are. It would probably be easiest if you send us your files.

In Skyline, you can use the menu item:
File > Share > (complete)
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:
https://skyline.ms/files.url

You should also send us at least one of your raw files (i.e. a pair of .wiff and .wiff.scan files)

Hopefully, setting the Explicit Retention Time will just work correctly.
-- Nick
 
kallo gergo responded:  2018-09-04 06:00
Thank you very much for your advice, now it works as it should be.

Thank you very much again!

Sincerely
Gergő Kalló