Hello Skyline Team,

Thank you for your continued development and user support for this great tool! We have been using Skyline as our primary tool for processing LC-MS data for several years. Unfortunately, we have recently encountered a problem that is effecting a seemingly random subset of our data. When we import raw data from an Agilent 6545 QTOF where both profile and centroid data were collected into Skyline with the "centroided" option selected as the precursor mass analyzer in the Full-Scan tab of the Transition settings, with some files, the MS1 spectra are lost and flat chromatograms appear for all transitions (see screenshot_centroid_1). When looking at the individual spectra within Skyline, it shows only SIM spectra (see screenshot_centroid_2). With other files acquired around the same time and with the same instrument (I included one example that worked and one that did not), this is not a problem. I have checked the raw data in other software and the centroided spectra are contained in the raw data of these problematic files. In troubleshooting this issue, I tried converting the file to mzML (with MSConvert) with CWT centroiding the data imports correctly into Skyline and the data looks fine. When I used MSConvert with vendor peak picking, the problem is not fixed. I also tried loading this file into Skyline with the "TOF" option selected as the precursor mass analyzer and 10,000 resolving power and the data loads correctly for all files. This issue seems to be isolated to centroid data. I have included two Skyline documents (one centroid, one profile), the raw data, transition list, and screenshots. Any help or advice on next steps on resolving this problem would be greatly appreciated.

Raw data and Skyline documents will be uploaded separately and linked.

Error has been reproduced on Skyline Daily (21.1.1.223) and Skyline (21.1.0.146) running on Windows 10.

Many Thanks!
-Ethan