Problem importing MS1 data ekaterina mostovenko  2019-12-09
 

Dear Skyline,

I am trying to import MS data acquired on Waters Synapt G2 Si and I keep on getting the following error:

"The file *.raw does not contain SRM/MRM chromatograms. To extract chromatograms from its spectra, go to Settings > Transition Settings > Full-Scan and choose options appropriate to the acquisition method used."

I set all settings in Full-Scan to none and I still get the same error.

I also tried to import DDA data, it was also unsuccessful, I did change my Transition Settings to DDA/TOF and got:

"No scans in *.raw match the current filter settings."

Does it mean that Skyline can't match spectra to the predicted transitions? Or am I doing something wrong?

Thank you!

 
 
Nick Shulman responded:  2019-12-09
If you want to import MS1 data, you need to go to:
Settings > Transition Settings > Full Scan
and change MS1 filtering Isotope Peaks Included to either "Count" or "Percent".

You might find it helpful to take a look at the MS1 full scan filtering tutorial:
https://skyline.ms/wiki/home/software/Skyline/page.view?name=tutorial_ms1_filtering

That tutorial shows how to start with DDA peptide search results and extract chromatograms for the peptides that were identified.

Most people who are using DDA with peptides have peptide search results. Skyline does not have a peptide search engine, but Skyline can read peptide search results from many popular peptide search engines. Here is a list of the peptide search result formats that Skyline understands:
https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

Hope this helps,
-- Nick
 
ekaterina mostovenko responded:  2019-12-09
Thank you, Nick! It was very helpful and I was able to load full scan data.