mProphet scores are usually calculated at the peptide level.
If you applied an isotope modification to the heavy peptide, and that modification had the "Relative retention time" set to "Unknown", then Skyline would calculate the mProphet scores separately for the light and heavy precursors. But, even in that case, the charge states of each label type would be considered together.
So, typically, all precursors under a peptide will have exactly the same mProphet scores. Those scores appear at the precursor level in the Document Grid because sometimes, depending on the isotope modifications you have in your document, the light and heavy scores might be different from each other.
If you wanted to get separate scores for your different charge states, one thing that you could do is delete everything but the charge 2 precursors from you document, and then do "Edit > Manage Results > Rescore" and then "Refine > Reintegrate" and see what scores all of the peptides got.
When Skyline is doing peak picking, Skyline always looks at the transitions for all of the charge states at the same time.
-- Nick |