The potential of mMass software search tool with new compound libraries was demonstrated on metabolomics of Scedosporium prolificans, S. apiospermum and Pseudallescheria boydii sensu stricto. Cyclic peptides pseudacyclins, small molecular weight tyroscherin analogues and various lipidswere detected by matrix-assisted laser desorption / ionisation mass spectral data of intact fungal spores, electrospray ionisation combined with tandem mass spectrometry was used for monohexosylceramide characterisation in fungal extracts.