Peak Picking Model for Small Molecules

Peak Picking Model for Small Molecules hogan  2019-05-28


I am attempting to use skyline as the data analysis software for small molecule quant assays. I have had good success but have found that even slight shifts in retention/aging columns results in a deterioration of skylines peak picking ability and makes it very difficult to automatically process the data using skyline runner. I see that the peak picking model is used to train the system for peptide peak analysis. Has there been any advances in using this model for small molecules?

Is there a way to tell skyline to pick the most intense, first, last, etc. peak in a desired retention time window to increase peak picking robustness?

As always, I love working with the software and am very excited about all the new features that have come out since I started using it. Thanks!


Brian Pratt responded:  2019-05-30
Hi Kyle,

Have you tried setting explicit retention times?

Also, for systematics retention time shifts like the column aging mentioned, you might look into iRT as a way of adjusting for systematic drift. We've long supported that for peptides, and recently added the capability for small molecules.

Thanks for using Skyline,

Brian Pratt