Dear Skyline team
I am trying to analyze hundreds of MRM dataset to use skyline, but I didn’t acquire the transitions of Decoy peptides in the MRM experiment in prior as suggested by the mprophet method. Can I still use the mProphet model for peak picking, or could you provide me some suggestions？Now, I just following the tutorial for manual evaluation.
I am wondering if can I automate pick manual peak and avoid of the bias (such as ( how good RT, ppm accuracy etc.)) by any statistical model? Do you have any suggestion to automate manual peak picking with statistical model for MRM dataset using Skyline?