Fig. 3: Mass spectrometry characteristics of FA cross-links.
From: Mass spectrometry reveals the chemistry of formaldehyde cross-linking in structured proteins
a The MS/MS fragmentation of a formaldehyde cross-link breaks the ion to its two peptides, each with an additional mass of 12 Da. The two peptides then break a second time to produce b- and y-fragments. b The MS/MS spectrum of a cross-link between two peptides of ovotransferrin. pepA and pepB are peaks matching the total mass of the corresponding peptides plus 12 Da. Peaks annotated with *b or *y match the masses of the corresponding b- and y-fragments plus 12 Da. For clarity, only peaks with intensities in the top quartile are shown. The annotation of the full spectrum is shown in Supplementary Fig. 3. c The two peptides identified in the above MS/MS spectrum are spatially close to each other in the crystallographic structure of ovotransferrin (PDBid 1OVT38). d The average number of cross-links identified for each formaldehyde concentration on a mixture of three proteins. Means and standard deviations calculated across three independent experiments, each with two technical replicates. The estimated false-detection rate is 3%. Source data are provided as a Source Data file.
