|IMS Predictor questions||Juan C. Rojas E.||2020-08-21|
Dear Skyline team,
I have a few questions I hope you can help me clarifying.
I checked at some point if the CCS areas reported in Skyline matched the ones calculated with Driftscope and I noticed slight differences. Maybe due to small differences in the application of the calibration equation stored in the files?
I import my DIA data with small retention time windows to limit false integrations and then run the predictor. However, after running the predictor I noticed that the EICs show the full chromatogram and not only the small retention windows imported in beginning.
I have tried using the automatic predictor and very often its determining incorrect offset estimations. In the image attached you can see that when automatic is ran it usually ends up with lots of positive offsets which is the complete opposite of what is expected from associated fragment ions in the HDMSE high energy scans. This happened because it chose same fragment ions that came from other co-eluting or closely eluting molecules.
Of course, with my manual corrections I still had some mistakes due to badly curated peaks, but at least the bias is towards negative offsets for most of them. I should mention that I use a low resolving power of 15 since is the value the encompasses all area for most of my molecules with my current instrument settings and analytes relative abundance.
Sorry if these were too many questions for one post, but I thought they were all related.