Retention time Prediction

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
sa825 responded:  2020-06-08
Hi Nick,
I was wondering id thgere was a tutorial for enabling this "Prosit" feature in Skyline?
I followed the instructions you put above but there is no "Prosit" under options?
Kaipo responded:  2020-06-08
Hi Shimon,
This feature was added pretty recently (Skyline 20.1). Can you verify that you're on this version (Help > About)?

sa825 responded:  2020-06-18
Hi Kaipo,

Thank you for your response. I have now been able to access Prosit and get spectra for peptides of interest.
My question now is how do I use the retention time prediction abilities of Prosit in Skyline?

Brendan MacLean responded:  2020-06-18
Hi Shimon,
You should learn a bit about iRT, which you can do with the iRT tutorial:

Or this video recording of a Skyline course session where I explain it:

For more detail on using Prosit, you can review my walk-through as part of the May Institute at Northeastern:

Good luck. There are a lot of online materials out there to help you learn more.