Hi support team,
I am working on an isotope tracing experiment where we used a DIA method on a Bruker Impact II instrument to record the data.
In general I am very satisfied on how skyline handles the data but I have a problem with some ion traces.
For example sample QC-pool_2: I have two Isomers listed in the Molecule List "MGDG". One traces for the second Isomer is shown, for the first it is not. Also, and this occurs for multiple molecules and samples, the ion trace is shorten on both sides. You can also see this in the example of MGDG and sample QC-pool_2.
I uploaded the skyline document with the name 'MS012_share.sky' to the share folder. Attached you find a screenshot from Bruker DA with the EIC of the MGDG and the raw data file of QC-pool_2 in case you need to reimport this particular sample.
I hope you have an idea what is wrong here.