|Peptide Mapping with Skyline||RuMa||2021-09-20|
Hi Skyline team,
I am trying to study the coverage of a biopharmaceuticals with Skyline. The goal is to digest the recombinant protein present in formulation and see if a full coverage can be obtained. The instrument used is a xevo qtof g2-xs and the data is acquired in MSE mode.
I would like to steer away from Biopharmalynx and use Skyline instead, but I find it hard to set parameters that can give me confidence in peptide identifications since I do not have a spectral library. I thought I could gain additional confidence with a predicted library using Prosit, but since the MSE mode does a ramp up of collision energy, a predicted library with a fixed CE was not helpful.
Do you have any suggestion, tutorial or paper I can refer to?