Chromatograms from SIM scans

Chromatograms from SIM scans michael plank  2019-01-13

Hi Skyline team,

apologies in case the answer to this is somewhere obvious that I missed.
I set up a PRM method where, in addition to the targeted MS2 scans, I`m recording an MS1 full-scan and for some of the precursors also (MS1) SIM scans (not for all precursors due to cycle-time considerations).
I was wondering: will Skyline automatically extract the MS1 chromatogram from the SIM scans where available or will it use the MS1 full-scan or both? Is there a way I can set how this should be handled?

Thanks a lot,

Tobi responded:  2019-01-24

Dear Michael,

just as a quick comment from my side without guarantee:

In our case we had files containing both SIM and Full Scan data. Skyline usually build chromatograms only for the SIMs from the raw files. To get chromatograms from the Full Scans we converted raw files to mzxml files using MS convert and additionally imported the mzxml files into the same or another skyline document. Might as well work with other file formats. Feel free to try it an write again if it does not work as described above.

Screenshot for freely available MS Convert and settings from a different post: