The invention relates to the acquisition of mass spectra of complex protein mixtures, often called protein profiles, for example to search for biomarkers which indicate stress situations, or to identify microbes. Up to now protein profiles have been acquired using ionization by matrix-assisted laser desorption with high detection sensitivity in linear time-of-flight mass spectrometers, but these display very poor mass resolution and a very poor reproducibility of the mass values. The invention provides methods which produce surprisingly similar mass spectra, but with far higher mass resolution and mass accuracy. Ionization takes place outside the vacuum at ambient pressure, preferably by means of laser desorption and CI post-ionization. Analysis of the ions takes place in a high-resolution mass spectrometer, for example a reflector time-of-flight mass spectrometer with orthogonal ion injection.