Fig. 2.

Best flyer peptide selection, transition selection, and FDR estimation. A, distribution of endogenously detectable best flyer peptides for the 16 proteins used as anchor points. B, 66 selected best flyer peptides were endogenously detectable by SRM with 4–14 transitions. C, the complete label-free SRM data set was scored using the algorithm mProphet, which takes into account information from measured target (gray) and decoy (black) peptide peak groups (31). Discrimination between target and decoy peptides led to an estimated FDR of ∼1%.