|Unable to extract chromatogram of the same ion in MS1 and MS2||Chris Ashwood||2018-11-26|
Dear Skyline support,
I hope you are all well. I am using the small molecule side of Skyline (most recent daily version and non-daily versions) and have encountered a limitation of Skyline that is present in both versions. If I set up my Skyline assay to integrate unfragmented precursor in MS2 scans, an extracted ion chromatogram of the precursor [M] is missing in MS1 but an extracted ion chromatogram of the precursor in MS2 is extracted. Other isotopic ions are detected, it's just the monoisotopic ion that is not being extracted.
I currently bypass this limitation by not including the unfragmented precursor in the fragment list but thought I would report it anyway.