Fig. 4: Possible fragments of DiSPASO during MS2 fragmentation and evaluation of MS Annika search setting regarding doublet distances.
From: Developing a new cleavable crosslinker reagent for in-cell crosslinking
A Fragmentation products of DiSPASO after high-energy collision dissociation (HCD) showing structures of DSSO-like cleavage products (alkene 11, ETFP 9 and ETHMP-fragments 10, main doublet) and possible additional doublets of the long side of the crosslinker (EMP 12 with SA 13 or T 14 as stubs, dotted gray box). B Numbers of residue pairs identified from Cas9 crosslinked with DiSPASO while searching with each doublet distance separately. D12 (ETHMP-alkene doublet) shows the maximum number of identified links with D11 (ETFP-alkene) as the second and D1, D2 (alkene-thiol, sulfenic acid-alkene) as the third abundant doublets. C Numbers of residue pairs identified from Cas9 crosslinked with DSBSO while searching with each doublet distance separately. D11 (ETFP-alkene doublet) shows the maximum number of identified links. The number of technical replicates is indicated as separate black dots on top of the bar (n = 3). The standard deviation was estimated as average distance from each data point to the sample mean. D Table of doublet definitions and delta masses of all possible doublets. E Table of substitutions and monoisotopic masses of all fragments including DiSPASO as full construct bound to peptides. IUPAC names of all compounds used in this manuscript are described in Supplementary Table S4.
