peptide prediction tool (stability and signal strength)

peptide prediction tool (stability and signal strength) gabriele philipps  2020-11-09


I have a rather general question which is not necessarily related to the Skyline software:
is there a software that can predict which peptides are better or worse suited for targeted proteomics (with respect to stability, retention time and above all signal intensity of the fragments which to my knowledge correlates with their ability to ionize)?
At the moment I know I should avoid cysteine and methionine and N-terminal glutamine and asparagine. But a tool which gives an overview on the peptide properties (when pasted in ) together with a judgement on the suitablility would be very helpful.

I hope you can help. Thanks for every suggestion.
Best regards,


Nick Shulman responded:  2020-11-09
There is an external tool available in the Skyline Tool Store called "Prego" which tries to choose peptide sequences which will perform the best in a mass spectrometer.

You can read the paper about the algorithm that it uses here:

-- Nick