Specific Cα-C Bond Cleavage of β-Carbon-Centered Radical Peptides Produced by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry

Transient Conformations Leading to Peptide Fragment Ion [c + 2H]+ via Intramolecular Hydrogen Bonding Using MALDI In-source Decay Mass Spectrometry of Serine-, Threonine-, and/or Cysteine-Containing Peptides

The formation of a peptide fragment ion [c + 2H]+ was examined using ultraviolet matrix-assisted laser desorption/ionization in-source decay mass spectrometry (UV/MALDI-ISD MS). Unusually, an ISD experiment with a hydrogen-abstracting oxidative matrix 4-nitro-1-naphthol (4,1-NNL) resulted in a [c + 2H]+ ion when the analyte peptides contained serine (Ser), threonine (Thr), and/or cysteine (Cys) residues, although the ISD with 4,1-NNL merely resulted in [a]+ and [d]+ ions. The [c + 2H]+ ion observed could be rationalized through intramolecular hydrogen atom transfer (HAT), like a Type-II reaction via a seven-membered conformation involving intramolecular hydrogen bonding (HB) between the active hydrogens (-OH and -SH) of the Ser/Thr/Cys residues and the backbone carbonyl oxygen at the adjacent amino (N)-terminal side residue. The ISD of the Cys-containing peptide resulted in the [c + 2H]+ ions, which originated from cleavage at the backbone N-Cα bonds far from the Cys residue, suggesting that the peptide molecule formed 16- and 22-membered transient conformations in the gas phase. The time-dependent density functional theory (TDDFT) calculations of the model structures of the Ser and Cys residues indicated that the Cys residue did not show a constructive bond interaction between the donor thiol (-SH) and carbonyl oxygen (=CO), while the Ser residue formed a distinct intramolecular HB.

Complete and selective nitration of tyrosine residue in peptides caused by ultraviolet matrix-assisted laser desorption/ionization

Complete and highly selective nitration of tyrosine (Tyr) as a residue-specific modification in peptides was found without side reactions, using ultraviolet matrix-assisted laser desorption/ionization (UV-MALDI) with a nitroaromatic reagent 3, 5-dinitrosalicylic acid (3,5-DNSA). The tyrosine nitration supported two propositions, namely, the UV-induced. NO₂ attack reaction mechanism by Long et al. and the C-NO₂ homolysis as a thermal process by Wiik et al. and Furman et al. With the UV-MALDI of peptides, a residue-specific reaction was observed in glycine (Gly) residue, i.e., an oxidation of the alpha-carbon of Gly due to attack of hydroxyl radical (.OH).

Cooperative dissociation of peptide backbones and side-chains during matrix-assisted laser desorption/ionization in-source decay mediated by hydrogen abstraction

Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) causes the selective cleavage of C_α -C peptide bonds when an oxidizing matrix is used, and the fragmentation involves the hydrogen abstraction from a peptide by a matrix. The hydrogen abstraction from either an amide nitrogen or β-carbon atom has been proposed to be the initial step leading to the C_α -C bond cleavage. In this regard, the production of [a]⁺ fragments originated upon bond cleavage at the C-terminal side of phenylglycine residues strongly suggested that that the C_α -C bond cleavage occurred through a nitrogen-centered radical intermediate and that the fragmentation through a β-carbon-centered radical intermediate can be ruled out from the MALDI-ISD process, because phenylglycine residues do not contain β-carbon atoms. The C_α -C bond cleavage of such nitrogen-centered radical initially produced an [a]•/[x - H] fragment pair, and then the [a]• radical either reacted with the matrix or underwent loss of the side-chain, leading to [a - H] or [d - H] fragment. The C_α -C bond cleavage at the C-terminal side of phenylglycine and phenylalanine residues only generated [a]⁺ fragments, whereas that of homophenylalanine and S-methylated cysteine residues provided both [a]⁺ and [d]⁺ fragments. The yield of [d]⁺ fragments was dependent on the chemical stability of the resultant radicals formed upon side-chain loss. MALDI-ISD produced [M - H + matrix]⁺ , [M - 16 + H]⁺ , [M - 32 + H]⁺ , and [d]⁺ fragments, when the analyte peptide contained a methionine residue. These fragments were formed upon abstraction of a hydrogen atom from the side-chain of a methionine residue and its subsequent reaction with the matrix. The oxidation of methionine residues suppressed the hydrogen abstraction from their side-chain.

Multiple Hydrogen Loss from [M + H]+ and [a]+ ions of Peptides in MALDI In-Source Decay Using a Dinitro-Substituted Matrix

The formation and radical-directed dissociation of multiple hydrogen-abstracted peptide cations [M + H - mH]·⁺ has been reported using MALDI-ISD with dinitro-substituted matrices. The MALDI-ISD of synthetic peptides using 3,5-dinitrosalicylic acid (3,5-DNSA) and 3,4-dinitrobenzoic acid (3,4-DNBA) as matrices resulted in multiple hydrogen abstraction from the analyte [M + H]⁺ and fragment [a]⁺ ions, i.e., [M + H - mH]⁺ and [a - mH]⁺ (m = 1-8). All of the ISD spectra showed unusually intense [a]⁺ ions originating from cleavage at the Cα-C bond of the Leu-Xxx residues when peptides without Phe/Tyr/His/Cys residues were used. The intensity of the [a_n]⁺ series ions generated using 3,5-DNSA and 3,4-DNBA rapidly decreased with increasing residue number n, suggesting cleavage at multiradical sites of [M + H - mH]^•+. It was suggested that multiple hydrogen abstraction from protonated peptides [M + H]⁺ mainly takes place from the backbone amide nitrogen.

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

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.