New Approach for Pseudo-MS<sup>3</sup> Analysis of Peptides and Proteins via MALDI In-Source Decay Using Radical Recombination with 1,5-Diaminonaphthalene

Abstract

Matrix-assisted laser desorption ionization in-source decay (MALDI-ISD) is a useful method for top-down sequencing of proteins and preferentially produces the <i>c</i>′/<i>z</i><sup>•</sup> fragment pair. Subsequently, radical <i>z</i><sup>•</sup> fragments undergo a variety of radical reactions. This work is focused on the chemical properties of the 1,5-diaminonaphthalene (1,5-DAN) adducts on <i>z</i> fragment ions (<i>z</i><sub><i>n</i></sub>*), which are abundant in MALDI-ISD spectra. Postsource decay (PSD) of the <i>z</i><sub><i>n</i></sub>* fragments resulted in specific peptide bond cleavage adjacent to the binding site of 1,5-DAN, leading to the preferential formation of <i>y</i>′<sub><i>n</i>–1</sub> fragments. The dominant loss of an amino acid with 1,5-DAN from <i>z</i><sub><i>n</i></sub>* can be used in pseudo-MS<sup>3</sup> mode to identify the C-terminal side fragments from a complex MALDI-ISD spectrum or to determine missed cleavage residues using MALDI-ISD. Although the N–C<sub>α</sub> bond at the N-terminal side of Pro is not cleaved by MALDI-ISD, pseudo-MS<sup>3</sup> via <i>z</i><sub><i>n</i></sub>* can confirm the presence of a Pro residue

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