Dear Skyline Team,
Thank you for your continued development of this excellent software package.
I am having trouble importing a timsTOF Pro file. The instrument was set up to collect scheduled PRM data for 34 isotope labeled peptides. When the results are imported into Compass DataAnalysis software, it appears that the method worked as anticipated - precursors are observed in the MS1 chromatogram and corresponding MS/MS are generated within the specified windows. However, when importing the results into Skyline Daily (220.127.116.11), no precursor and no product ions are found.
I've successfully imported other targeted runs from the timsTOF. Only this scheduled method is causing problems. Any insight you can provide would be appreciated. Thanks.