Generating library manual from PRM runs

Generating library manual from PRM runs tsveth  2019-11-19

Hi everybody,

During development of my HL library sometimes software (MQ, PD, etc) does not detect peptides even though they can clearly be found in the spectra. Is it possible to load my PRM runs into Skyline and manually select the spectra that should be used for the library by using the Skyline chromatograms?

Thank you!

Nick Shulman responded:  2019-11-19
I am not sure I understand your question.

Skyline does have the menu item:
File > Export > Library
which creates a .blib file where the "spectra" are simulated using the chromatogram peak areas of all of the transitions in your Skyline document.

A different thing that you can do, if you want to create spectral library from some raw files and a list of spectra, you can create what we call a ".ssl" file (which stands for "spectrum sequence list"). There is a description of what to put in that file here:

-- Nick