Further studies of in-source fragmentation of peptides in matrix-assisted laser desorption-ionization

A variety of additional factors that influence the in-source fragmentation of MALDI ionized peptides have been studied. In an attempt to further understand this in-source fragmentation process, instrumental parameters such as the desorption laser pulse width and wavelength, and ion-extraction delay period have been examined as to their effect on peptide fragmentation. Use of a shorter desorption wavelength (266 nm) increases the intensity of in-source fragment ions (relative to the intact protonated molecular ion species), but does not change the types of fragment ion series that are observed. Essentially, no differences in the fragmentation spectra were observed when the laser pulse width was varied (700 ps versus 5 ns) and a constant (337 nm) desorption wavelength was employed. In addition, both positive-and negative-ion in-source fragmentation spectra for several matrices were examined. The previously reported c(n) and y(n) in-source fragment ion series are very similar as to occurrence and intensity in both positive-and negative-ion mode MALDI spectra. This similarity in positive-and negative-ion mass spectra suggests that in-source fragmentation most probably occurs independent of the ionization pathway (protonation or deprotonation) and is therefore not linked to the "exothermicity" of the proton transfer reaction as previously suggested. Possible alternative ion activation processes are discussed. A new "a(n)-type" ion fragment series has also been identified and is more prevalent with certain classes of MALDI matrices. Finally, in-source fragmentation can be suppressed by certain MALDI matrices. Super-DHB almost completely suppresses y(n)-series fragment ions relative to DHB. The c(n)-series fragment ions are also reduced in relative intensity but are still observed. Alpha-cyano-3,4,5-trimethoxy cinnamic acid is shown to almost completely suppress both of the c(n) and y(n) fragmentation ion series. (C) 1997 Elsevier Science B.V.