Estimation of peptide N-Cα bond cleavage efficiency during MALDI-ISD using a cyclic peptide

Experimental and Theoretical Investigation of MALDI In-Source Decay of Peptides with a Reducing Matrix: What Is the Initial Fragmentation Step?

Matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) with a reducing matrix is believed to be initiated by hydrogen transfer from the matrix to the peptide. Several new matrices have recently been developed to achieve more efficient MALDI-ISD. In particular, the use of matrices containing aniline groups facilitates MALDI-ISD to a greater extent than that of matrices containing phenol groups, although the N-H bond in aniline is stronger than the O-H bond in phenol. In this study, photoelectron yield spectroscopy of matrix solids revealed that conversion of the phenol group to the aniline group decreased the ionization energy of the matrix solids. Crucially, the use of a matrix with lower ionization energy has been found to result in efficient cleavage at N-Cα and disulfide bonds by MALDI-ISD. Therefore, electron association with the peptide rather than the fragmentation mechanism involving hydrogen atom attachment is proposed as the initial step of the MALDI-ISD process. In this mechanism, electron transfer from the reducing matrix to the peptide produces a peptide anion radical, which provides either a [c_n + H]/[z_m]• or [a_n]•/[y_m + H] fragment pair. Fragmentation of the peptide anion radical strongly depends on the gas-phase acidity of the matrix used. Subsequently, the resultant fragments/radicals underwent a reaction in the MALDI plume, producing observable even-electron ions. Consequently, MALDI-ISD fragments are observed as both positive and negative ions, even though MALDI-ISD with a reducing matrix involves fragmentation of peptide anion radicals. The proposed mechanism is suitable for obtaining a better understanding of the MALDI-ISD process.

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.

Ultraviolet-Laser-Induced Electron Transfer from Peptides to an Oxidizing Matrix: Study of the First Step of MALDI In-Source Decay Mass Spectrometry

Although the N-H bond in peptide backbones is stronger than the C-H bond, hydrogen abstraction from the amide nitrogen is considered to be the initial step in the C_α-C bond cleavage of peptide backbones by matrix-assisted laser desorption/ionization in-source decay (MALDI-ISD) when using an oxidizing matrix. MALDI-ISD induces C_α-C bond cleavage in most amino acid residues, whereas the N-terminal sides of proline (Pro) residues preferentially undergo peptide bond cleavage, which cannot be explained by the previously proposed mechanism involving hydrogen abstraction from peptides. To explain the whole MALDI-ISD process, electron abstraction from peptides by the oxidizing matrix is proposed as the initial step in the MALDI-ISD process. The electron abstraction occurs from either nitrogen or oxygen in the peptide backbone and induces the cleavage of both C_α-C and N-H bonds in most amino acid residues, except for those on the N-terminal sides of Pro residues. Electron abstraction from the Pro residues induces the cleavage of both peptide and C_α-C bonds, which is consistent with MALDI-ISD experimental results. The electron transfer from the peptide to the oxidizing matrix occurs simultaneously with the formation of matrix ions, which is considered to be the initial ion formation process in MALDI. The resultant peptide radical cation produces protonated and neutral molecules/radicals, which undergo subsequent ion-molecule reactions in the MALDI plume, finally yielding the ions that are observed in MALDI-ISD spectrum. As a result, the fragment ions formed by MALDI-ISD are observed as both positive and negative ions.

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.

Fundamental study of hydrogen-attachment-induced peptide fragmentation occurring in the gas phase and during the matrix-assisted laser desorption/ionization process

Mass spectrometry with hydrogen-radical-mediated fragmentation techniques has been used for the sequencing of proteins/peptides.

Activation of Reactive MALDI Adduct Ions Enables Differentiation of Dihydroxylated Vitamin D Isomers

Vitamin D compounds are secosteroids, which are best known for their role in bone health. More recent studies have shown that vitamin D metabolites and catabolites such as dihydroxylated species (e.g., 1,25- and 24,25-dihydroxyvitamin D₃) play key roles in the pathologies of various diseases. Identification of these isomers by mass spectrometry is challenging and currently relies on liquid chromatography, as the isomers exhibit virtually identical product ion spectra under collision induced dissociation conditions. Here, we developed a simple MALDI-CID method that utilizes ion activation of reactive analyte/matrix adducts to distinguish isomeric dihydroxyvitamin D₃ species, without the need for chromatography separation or chemical derivatization techniques. Specifically, reactive 1,5-diaminonaphthalene adducts of dihydroxyvitamin D₃ compounds formed during MADI were activated and specific cleavages in the secosteroid's backbone structure were achieved that produced isomer-diagnostic fragment ions. Graphical Abstract ᅟ.

Direct MALDI-MS analysis of the disulfide bonds in peptide using thiosalicylic acid as a reactive matrix

The ability of a thiol-containing molecule, thiosalicylic acid (TSA), to function as a reactive matrix for matrix-assisted laser desorption/ionization (MALDI) mass spectrometry analysis of peptides has been investigated. Although TSA has reducing characteristics, the use of TSA did not cause a reduction-induced MALDI in-source decay, probably because of the weak interactions between the thiol group in TSA and the carboxyl oxygen in the peptide. In contrast, when peptides containing disulfide bonds were analyzed by MALDI with TSA as the matrix, the disulfide bond was partially cleaved owing to the reaction with TSA, producing TSA-adducted peptides. The reaction between the disulfide bond and TSA was suggested to be occurred in solution. The comparison of the MALDI mass spectra obtained using conventional matrix and TSA allows us to count the number of disulfide bonds in the peptides. Copyright © 2017 John Wiley & Sons, Ltd.