Exporting mirror plot dotp values

Exporting mirror plot dotp values sven.van.bael  2020-02-04

Hi Skyline team

When comparing two spectral libraries using the mirror plot option, a dotp comparing the individual spectra from each library is calculated (see example attached). Is there a way to export these comparison dotp values for all peptides at once? (i.e. is there an option to do this via Document Grid?)

Many thanks!

Brendan MacLean responded:  2020-02-04

There is not yet. I think you are the second to request this.

We are likely to extend our Prosit integration in coming releases, since this is our very first and there are both interesting new advances in Prosit prediction (like proteotypicity, precursor charge, and CCS) and obvious omissions (like no mirror plots in View > Spectral Libraries).

We will keep this request in mind. To do it well, we would need to implement a BackgroundLoader, like the one we have for protein metadata which would automatically query the Prosit interface for predictions and perform this calculation or store the full spectra on the document tree.

At present, the mirror spectra are requested at display-time for the plot you are showing and each dotp value is calculated individually in the plotting code.

I believe the other request we have heard is for other kinds of dotp calculations, like only including peaks with annotated signal in both spectra, which again would require either storing the multiple values on the document tree or the entire predicted spectrum to allow for on-demand calculation. We really don't want to be querying Prosit on-demand in order to fill out the Document Grid.

Thanks for your feedback. We definitely expect to continue improving Prosit integration with Skyline. Stay tuned.