LAUSR

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 Cα-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 Cα-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 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 Cα-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 Cα-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.