Complementary Sequence Preferences of Electron-Capture Dissociation and Vibrational Excitation in Fragmentation of Polypeptide Polycations

摘要

Electron-capture dissociation (ECD)[1] of polypeptide polycations produces preferential cleavage of the backbone NC bond (c, z fragments), while fragmentation based on vibrational excitation (VE) of the same ions (for example, collision-activated dissociation (CAD), infrared multiphoton dissociation (IRMPD), or surface-induced dissociation (SID)) gives preferential CN cleavage (b, y fragment ions). Both types of fragmentation phenomena show preferences for the context of the amino acids. For example, VE has a strong preference for the N-terminal side of proline and the N-terminal side of aspartic acid.[2] More subtle preferences in CAD have been studied recently on a large data set.[3] Cleavage on the N-terminal side of Pro by ECD are absent because of the tertiary amide nitrogen atom.[1] Preferential cleavage on the C-terminal side of tryptophan has been reported,[4] but in general it has been unclear whether amino acid preferences in ECD are similar to those in CAD.[4] This question has both fundamental and application-related aspects. According to the generally accepted theory,[5] cleavage of CN bonds by VE are induced by a mobile proton solvated by backbone amides. The presence of a proton at the amide nitrogen atom greatly weakens the amide bond,[5] and can also reduce the strength of other nearby bonds.[6] Thus, cleavage of the amide bond by VE is a local phenomenon with respect to the proton location. Both local[1], [7] and nonlocal[8]-[11] cleavage mechanisms have been suggested for ECD. According to the local ECD model, the NC bond next to the position of the neutralized proton is cleaved. Thus, ECD may be expected to have similar preferences as VE for amino acid contexts (except proline). The practical aspect of this issue is the use of CAD and ECD in tandem mass spectrometry, an important tool for proteomics. Application of two fragmentation methods instead of one is only advantageous if the methods are complementary in terms of sequence preferences.