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Analyte incorporation and ionization in matrix-assisted laser desorption/ionization visualized by pH indicator molecular probes.

Despite the spreading applications of matrix-assisted laser desorption/ionization (MALDI), its fundamental understanding is still limited and under constant debate. This report focuses on the initial state of the analyte in the host matrix. pH indicator dyes serve as molecular probes since their color directly indicates their (de)protonation state. For a set of matrixes at their intrinsic pH, solution color was maintained, delivering clear proof for analyte incorporation in the solution charge state. Moreover, substantial solvent inclusion is determined by 1H NMR spectroscopy. MALDI mass spectra show a clear correlation to the dye charge state. However, the dominant solution species are not observed exclusively in the mass spectra, pointing to a proton transfer or proton neutralization activity of the matrix.