Retention time Prediction scv01958  2020-04-23


I had a question regarding the retention time prediction tool of Skyline. I understand that the tool is capable of using imported data to calibrate a calculator and build up an iRT database. This iRT database is then very useful in validating retention times recorded in future trials. However, I am confused on the "prediction" capabilities of this tool. Let's say I have a calibrated calculator already made consisting of an iRT database of related peptides/molecules. I have a new peptide/molecule that is related, but slightly different in some way, the difference is a change in structure or charge. Will this calculator be able to predict the retention time of my new compound based on the database I have already built?


Nick Shulman responded:  2020-04-23
When Skyline uses the term "Prediction", it is not talking about predicting the retention times of peptides that have not been measured before. Instead, it is talking about scaling the observed iRT values in order to predict the retention times of those same peptides in a longer gradient, or some other situation that might cause the retention times to be scaled by a linear equation.

Skyline 20.1 did recently integrate a web service called "Prosit" which really does do retention time prediction based on amino acid sequences.
I am not sure where to find documentation about how to use Prosit in Skyline. I know that you have to first go to:
Tools > Options > Prosit
and choose some things from the dropdowns in order to enable this feature in Skyline.
-- Nick