Is there a way to use skyline to predict peptides in neg ion mode (precursors and transitions?)
Brian Pratt responded:
Yes, you can specify negative charges in your transition list. Skyline will use only negative mode mass spec data when extracting chromatograms for those (and vice versa for positive charged precursors, of course).
Let me know if you have other questions.
Thanks for using the Skyline support board,
Nick Shulman responded:
Skyline only supports positive charges on peptides.
If you want to use negative charges with peptides, you would need to pretend to Skyline that these are small molecules, and you would need to specify the precursor and products as either m/z values or chemical formulas.