Effect of gas pressure and gas type on the fragmentation of peptide and oligosaccharide ions generated in an elevated pressure UV/IR-MALDI ion source coupled to an orthogonal time-of-flight mass spectrometer.

Matrix-assisted laser desorption ionization (MALDI) allows for the mass spectrometric (MS) analysis of thermally labile, non-volatile biomolecules. However, some residual analyte fragmentation typically accompanies the phase transition from the condensed to the gas phase and following plume expansion, even under optimized conditions. In-source decay (ISD) and post-source decay (PSD) MALDI MS are two techniques that make use of these phenomena and that can provide useful structural information by producing characteristic fragment ions of the analyte compounds. In orthogonal extracting time-of-flight mass spectrometry (o-TOF-MS), the pressure of the cooling gas in the ion source has a strong influence on the extent of analyte ion fragmentation. We investigated the effect of this parameter on peptide and oligosaccharide fragmentation by examining a range of pressures (from 0.05-1.8 mbar) in combination with seven different buffer gases (He, Ne, Air, N-2, CO2, CH3, isobutane). Ions were generated by ultraviolet (UV) and/or by infrared (IR) MALDI. The influence of the ion extraction voltage on the analyte fragmentation also was investigated for a selected set of gas parameters. We observed that individual fragment ions exhibit characteristic fragment yield-pressure dependencies that can be classified into three groups. Type I ions resemble species that are also found in MALDI PSD MS analysis, while type II ions resemble typical ISD fragments. The yield-pressure relationship of type III ions suggests that these are the result of a combination of both processes. Comparing the yields of fragmentation for the different buffer gases reveals a correlation between their internal degrees of freedom and their collisional cooling efficiency. Changing the buffer gas pressure and/or extraction field provides an easy means to influence analyte ion fragmentation and to switch from the primary production of one type of fragment species to another. The method can therefore facilitate the structural characterization of MALDI-generated ions.