General Mechanism of Cα–C Peptide Backbone Bond Cleavage in Matrix-Assisted Laser Desorption/Ionization In-Source Decay Mediated by Hydrogen Abstraction

• Published in: Journal of the American Society for Mass Spectrometry 2019-08, Vol.30 (8), p.1491-1502
• Main Author: Asakawa, Daiki
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Analytical Chemistry; Beta decay; Bioinformatics; Biotechnology; Carbon; Carbon - chemistry; Chains; Chemistry; Chemistry and Materials Science; Cleavage; Decay; Density functional theory; Desorption; Deuterium; Electron capture; Electrons; Fragmentation; Fragments; Hydrogen; Hydrogen - chemistry; Ionization; Ions; Mass spectrometry; Models, Molecular; Nitrogen; Organic Chemistry; Oxidation; Peptides; Proteomics; Radicals; Research Article; Scientific imaging; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Spectroscopy; Structural analysis; Substance P - chemistry; Temperature; Transformations
• ISSN: 1044-0305; 1879-1123
• DOI: 10.1007/s13361-019-02214-6

Nitrogen-centered and β-carbon–centered hydrogen-deficient peptide radicals are considered to be intermediates in the matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD)–induced C α –C bond cleavage of peptide backbones when using an oxidizing matrix. To understand the general mechanism of C α –C bond cleavage by MALDI-ISD, I study the fragmentation of model peptides and investigate the fragment formation pathways using calculations with density functional theory and transition state theory. The calculations indicate that the nitrogen-centered radical immediately undergoes C α –C bond cleavage, leading to the formation of an a •/ x fragment pair. In contrast, the dissociation of the β-carbon–centered radical is kinetically feasible under MALDI-ISD conditions, leading to the formation of an a / x • fragment pair. To discriminate these processes, I focus on the yield of d fragments, which originate from a • radicals through radical-induced side-chain loss, not from a fragments. The C α –C bond cleavage on the C-terminal side of the carbamidomethylated cysteine residue is found to produce d fragments instead of a fragments. According to the calculation of the rate constant, the corresponding fragmentation occurs within 1 ns. The intense signal arising from d fragments and the lack of or weak signal from a fragments strongly suggest that the C α –C bond cleavage occurs through a nitrogen-centered radical intermediate. In addition to the side-chain loss, the resulting a • radical undergoes hydrogen atom abstraction by the matrix. The results for a deuterium-labeled peptide indicate that the matrix abstracts a hydrogen atom from either the amide nitrogen or the β-carbon.