dotp / rdotp between samples

dotp / rdotp between samples Juergen  2020-06-23

Dear Skyline team,

I currently use PRM in the identification of several peptides. My reference peptides are, however, not labeled and hence I measure them in separate runs. I know it is possible to get dotp values for each measurement in comparison to the corresponding library spectrum but I would prefer the dot product of the selected transitions in comparison to my control run (similar to the rdotp value for labeled and unlabeled peaks within one run). Is it possible to get this value?

I would like to use this value instead of the dotp against the library spectrum because I guess that than all the MS2 spectra below the peak would count for the calculation, while in the library only those spectra are retained that are nicely identified.

Best regards,

Nick Shulman responded:  2020-06-23

I am not sure that I understand your question, but you might be able to achieve what you want using the "File > Export > Spectral Library" menu item.
The Export Spectral Library command creates a .blib file, where the "spectra" are made using the transitions in your Skyline document and their chromatogram peak areas.
You could start with a Skyline document that only contains your control run. Then, you can use the Export Spectral Library to create a .blib file based on the peak areas in that control run. Then, if you use that .blib file in a Skyline document with your other runs, the library dot product will be the dot product between the other run and the control run.

-- Nick
Juergen responded:  2020-06-23
Dear Nick,

Thank you! This was exactly what I was looking for.
I was not aware of the option to build a .blib file from chromatograms.