Fig. 2.

Manual examination of MS/MS spectra. A, the MS/MS spectrum of conantokin-fla was manually examined against three possible conantokin sequences without the PTMs that are present in the precursor ion. The mass accuracy of each spectrum was calculated with the mass of the precursor ion with corresponding PTMs shown in each spectrum heading. The third sequence was taken as the most confident result. B, the MS/MS spectrum of fla6e was automatically annotated (panel i) and then manually assigned (panel ii) by introducing point mutations of T11S, G23T, and L28V (shown in cyan in the inset sequences). Interfragmented ions were also manually labeled. In this figure, as well as in Fig. 3 and Fig. 4, the orange letters in the inset sequences indicate the residues with modifications listed in each spectrum heading.