Accurately measured monoisotopic mass of a biomolecule can reveal its elemental and, in the case of a biopolymer, its monomer composition. In this work, the limitations of the technique were analyzed in application to peptides. For the currently available level of mass accuracy of about(1 ppm, the mass limit for revealing the unique elemental composition of a peptide was found to be 700-800 Da, with the possibility to extend this range as the mass accuracy improves. As for the amino acid composition determination, the principal limit of ∼500-600 Da cannot be overcome in the general case by instrumental or methodological improvements. It is proposed that, for the peptide characterization, the molecular mass must be determined with sufficient accuracy to rule out a significant fraction of the peptides having the same nominal mass but different elemental and amino acid compositions. An accuracy of (1 ppm was found to exclude 99% of such peptides and, therefore, ensure a high degree of confidence in peptide characterization.

Measurements of kinetic energy distributions of molecular ions ejected into an extraction field by matrix-assisted laser desorption are reported. The measurements were made in a time-of-flight mass spectrometer with an electrostatic mirror by measuring the reflected signal as a function of the difference between the accelerating voltage and the voltage applied to the mirror. The molecular ions were found to have less kinetic energy than the extraction field alone would normally provide, i.e., we observed an energy deficit. Under conditions typical for a matrix-assisted laser desorption experiment, the deficit is about 24 eV for molecular ions of insulin. The size of the deficit increases with the intensity of the molecular ion signal, and the molecular weight of the protein; it is also larger for negative molecular ions than for positive molecular ions.

A quartz crystal microbalance (QCM) is employed to determine the desorption yield of neutral particles in matrix-assisted laser desorption ionization. For ferulic acid, the matrix substance used, the QCM mass resolution of 1 ng corresponds to a detection limit of =loL2 particles. Sample exposure effects are studied at different fluences by measuring the total desorption yield after consecutive laser pulses fired on the same spot on the sample. The dependence of the total yield on the fluence is studied for different angles of incidence of the laser beam. Varying the distance between the QCM and the sample yields information about the angular spread of the desorbed neutral particles. Additional information about the fluence threshold for the production of charged particles is gained by direct electronic measurements of sample charging.

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