Fungi cause diseases of important crops. Their diagnostics is based on host specificity, symptoms and microscopy. Our joined team recently investigated an alternative based on intact cell mass spectrometry. This requires only a small amount of the material and takes the advantage of easy sample processing and fast data interpretation. Using two model pathogens, we have developed a methodology for both sample preparation and measurement on the instrument. For around ten microorganisms, we have obtained a library of protein mass spectra, which is available for taxonomic identification of field isolates. In the frame of a continuation project, we would like to finalize the methodology for biotyping of plant pathogens by direct measurements from infected material (leaf, stem) that would allow fast, cheap and reliable diagnostics. The studied microorganisms will be extended to pathogens of hop and grapevine. We also plan to discover infection biomarkers using detailed analysis of fungal surface proteins.