The mechanism of in-source decay (ISD) in matrix-assisted laser desorption/ionization (MALDI) has been described. The MALDI-ISD with an oxidizing matrix is initiated by hydrogen abstraction from peptides to matrix molecules, leading to hydrogen-deficient peptide radicals. Subsequently, the C-alpha-C and C-alpha-H bonds are cleaved, forming the a center dot/x fragment pair and [M-2H], respectively. Those reactions competitively occur during MALDI-ISD processes. Our results suggest that the C-alpha-H bond cleavage to form [M-2H] was induced by collisions between hydrogen-deficient peptide radicals and matrix molecules in the MALDI plume. In contrast, the C C bond cleavages occur via a unimolecular dissociation process and independently of the collision rate in the MALDI plume. The formation mechanism of the a-, b-, and d-series fragments are also described. We report 2,5-bis(2-hydroxyethoxy)-7,7,8,8-tetracyanoquino-dimethane (bisHE-TCNQ), being known as an organic semiconductor and an electron acceptor, as a novel suitable matrix for the MALDI-ISD of peptides via hydrogen abstraction.