Dear Skyline team,
could you please give out some information regarding overlap DIA? You recommended to use MSConvert to demultiplex DIA data with overlap. However, MSConvert usually results in an error message:
Failed - System.Exception: SpectrumToIndices() Number of demultiplexing windows changed. Minimum window size or window boundary tolerance may be set too low.
Is this because of acquiring the DIA with overlap and with margins? I also noticed when having overlap DIA with margins that those margin sizes can slightly differ in size after window placement optimization, could that be another potential issue?
I know that potential debugging MSConvert is not your job, but can you please tell me which variants of overlap SWATH you tested and what sould be working (margins, optimized placement...).
If you are interested please find the uploaded raw file for you to read the DIA scheme.