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About one in seven German citizens is suffering from respiratory allergies, which are mainly caused by anemophilous plant pollen. These pollen grains are monitored to provide a national information network. Their conventional identification is performed by time-consuming microscopic examinations based on the genus-specific pollen morphology. A variety of spectroscopic and spectrometric approaches have been proposed to develop a fast and reliable pollen identification using specific molecular information. Amongst them, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) showed a high potential for the successful investigation of such complex biological samples. The evaluation of the obtained peak patterns from pollen mass spectra with multivariate statistics enables a consistent and rapid identification of the taxonomic relationships.