Matrix-dependent a/x pair and overdegraded w/y/z ions generated by radical-directed dissociation of peptide radical cations [M] in matrix-assisted laser desorption/ionization in-source decay.

Fragmentation of peptide radical cations [M] has been examined using matrix-assisted laser desorption/ionization (MALDI) in-source decay (ISD) with hydrogen-abstracting nitro-substituted matrices. The ISD spectra of peptides containing an arginine (Arg) residue at carboxyl (C)-termini showed preferential [w] ions when 4-nitro-1-naphthol (4,1-NNL) matrix was used, whereas the use of 3,5-dinitrosalicylic acid (3,5-DNSA) resulted in preferential [x] ions. Minor or some [d] , [x] , [y] , and [z] ions were also observed. For peptides containing Arg residue at amino (N)-termini, the ISD spectra showed preferential [a] ions independent of matrix used. The observed [a] , [w] , [x] , [y] , and [z] ions can be rationally explained by radical-directed dissociation (RDD) of the peptide radical cations [M] , although [d] ions may be formed via Norrish Type I cleavage and/or by RDD of [M] ions. The formation of overdegraded [d] , [w] , [y] , and [z] ions is discussed from the standpoint of the internal energy of radical cations [M] and radical fragment ions [a + H] and [x + H] deposited via collisional interactions with excited matrix molecules in the MALDI plume. The radical site of the peptide cations [M] was presumed to be backbone amide nitrogen, from MALDI-ISD data with three different deuterated amino acids.