Fig. 1.

PIR structure. a, conceptual modular design of novel cross-linkers, PIRs. b, the specific fragmentation pattern of PIR-labeled peptide distinguishes dead-end, intra-, and intercross-linked peptides. The neutral mass of the precursor ion equals the sum of the neutral masses of its product ions. c, structure of a biotinylated Rink-based PIR. The singly and doubly charged reporter ions are 1122.5 and 561.7, respectively. d, structure of a biotinylated DP-based PIR. The MSMS labile bonds are indicated by the dashed lines, the reactive groups are NHS esters, and the affinity group is biotin. The singly charged reporter ion is 752.4.