Figure 1.

Schematic summary of high‐density cross‐linking/mass spectrometry experiments in CASP11. We incubate the target protein with the sulfo‐SDA cross‐linker. During incubation, the cross‐linker reacts with lysine, serine, threonine, tyrosine, and the protein N‐termini at one end. Upon activation with UV light, the other side of the linker forms a reactive carbene species and reacts with any other amino acid in close proximity. We then digest the protein using proteases. In the analysis step, we subject the peptide mixture to mass spectrometric analysis. We match the mass spectra to theoretical spectra of sequence fragments derived from the target sequence. The output of this procedure is a list of cross‐linked residues.