Extended Data Fig. 4: FragPipe diagnostic ion miningcoupled with MSFragger mass offset search identify signature fragment ions for the SEE-CITE modification.
From: Small-molecule binding-site discovery using silyl ether-enabled chemoproteomics
A, Shows proposed structures of signature fragment ions with exact masses corresponding to the m/z values identified by diagnostic ion mining for entry 6 from Fig. 2c. B, Frequency distribution and C, relative intensities of signature fragment ions. D, The presence of unshifted ions for the C-terminal half of the peptide enables partial localization of the SEE-CITE modification to the N-terminal ‘lrdtdt’ portion of the peptide, as illustrated by the lower spectra, where the modification was manually placed on the 8D residue (bottom) rather than the 1 L residue (top), which results in a decreased number of matched unshifted Y ions, with loss of the Y7 and Y8 fragments. E, shows hyperscores derived from unshifted ions for the lrdtdtLDLSGPAR peptide DHX16, for which no shifted ions were matched. Experiments were performed in duplicate. All data can be found in Supplementary Table 4.
