• Sign In
  1. Requests

Full MS and t-SIM in the same RAW file: how can we download the full MS in Skyline?

support

View Request

view list print
Full MS and t-SIM in the same RAW file: how can we download the full MS in Skyline? lucille stuani  2025-02-06 11:58
 

Hi Skyline support,

I'm a new user of skyline and really loving it. Thanks so much for this amazing tool!

However, I have a problem with uploading the full MS data from my raw file (Q-Ex Thermo) as I also have a t-SIM on the method on the 2 first minutes only to measure an internal standard we spike in and that is not in the range of our full MS method. When I upload the raw data on Skyline, I only see the t-SIM in the first 2 minutes. I saw a previous support ticket with a similar problem and they advice to convert in mzML file and then upload again to see the full MS but it did not work for me; still seeing only the t-SIM scan.

Do you by any chance have another solution I could use?

Thanks a lot in advance for your help and answer.

Best,
Lucille
 
 
Nick Shulman responded:  2025-02-06 12:06
If you go to the "Full Scan" tab at "Settings > Transition Settings" there is a "Ignore SIM Scans" checkbox which might fix your problem.
After you check the checkbox you will need to tell Skyline to extract chromatograms again using the "Reimport" button at "Edit > Manage Results".
That checkbox causes Skyline to ignore all spectra where the scan range was less than 500 m/z wide.

There is a possibility that the "Ignore SIM Scans" checkbox might cause all of your MS1 spectra to be thrown out if your method, in which case we would recommend using Skyline-daily and following the instructions in the following support request:
https://skyline.ms/announcements/home/support/thread.view?rowId=68218
-- Nick
 
lucille stuani responded:  2025-02-06 12:38
Thanks so much Nick; it works by ignoring the SIM. Thanks a lot for your super quick answer.

I guess there is no way to upload in the same skyline analysis my files with the t-SIM to use the spiked standard as surrogate standard?

Thanks again.

Best,
Lucille
 
Nick Shulman responded:  2025-02-06 12:48
I am not sure I understand your question.
If you are asking whether it's possible to have one set of chromatograms in the document which are extracted from t-SIM spectra, and another set of chromatograms extracted from regular spectra, then you should create separate Precursor's in the Targets tree that have different Spectrum Filter's on them.
You can read about spectrum filters here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=SpectrumFilters

If your question was about surrogate standards you might find the answer here:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=Surrogate%20Standards
-- Nick