Review article Performance of MALDI-TOF MS platforms for fungal identification Carole Cassagne, 1,2 Anne-C ecile Normand, 1 Coralie L’Ollivier, 1,2 St ephane Ranque 1,2 and Renaud Piarroux 1,2 1 Parasitology and Mycology, Assistance Publique-H^ opitaux de Marseille, CHU Timone-Adultes, Marseilles CEDEX 5, France and 2 Aix-Marseille University, UMR MD3 IP-TPT, Marseilles, France Summary Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) is increasingly used by clinical microbiology laboratories to cope with the need for rapid, cost-effective and accurate identification of microorganisms. Several research teams have recently succeed in identifying moulds using MALDI-TOF MS, which was first adapted to bacteria, then to yeast identification. Since 2004, different commer- cial firms have released several ready-to-use MALDI-TOF MS platforms. This review describes the similarities and differences between the commercially available systems. In two parts, we first describe and compare the preprocessing and identification steps between the platforms and then compare the identification efficacy of yeast, moulds and dermatophytes species. Key words: dermatophyte, mould, yeast, clinical laboratory, MALDI-TOF mass spectrometry, diagnostic. Introduction Over the course of the last decade, Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-TOF MS) has enabled rapid and accurate identification of many microorganisms. MALDI-TOF MS was first adapted for the identification of bacteria, 1 and the tech- nique was later adjusted for yeast. 2 Recently, combined efforts by several mycological research teams have demonstrated that the method could also be successfully adapted to filamentous fungi identification, provided that adequate reference spectrum libraries were estab- lished and made available for routine laboratories. 3–7 For microorganism identification, MALDI-TOF MS involves an initial ionisation step and the separation of molecules based on the mass to charge ratio (m/z). This analysis results in a mass spectrum, which is usu- ally summarised in a graph plotting the m/z and the relative intensity of each ionised molecule on the x- and y-axis respectively. 8 A nitrogen laser is first applied to microorganisms embedded in an organic matrix. Compounding molecules of the microorgan- isms are then desorbed from the support, vaporised and ionised. The ionised molecules in the gaseous form are subsequently accelerated through an electrical field and then migrated in a vacuum tube at a velocity pro- portional to the m/z ratio. A detector at the end of the vacuum tube detects the ionised migrating molecules and measures their ‘time of flight’ and abundance over time. A raw spectrum is then preprocessed and com- pared against a database of known reference spectra. Based on the similarity of the sample spectrum to the reference spectrum, the microorganism is identified as belonging to the same genus, species or sub-species of the best-matched reference spectrum. The development of this technology has been a rev- olutionary achievement for medical laboratories and an undeniable progress for patient care due to the accuracy and speed of species identification. 1 However, MALDI-TOF MS implementation requires a good understanding of the principles underlying this tech- nology. In particular, the choices made by companies that market the devices and software can have conse- quences on the evolution of mycological diagnoses that potential users must anticipate when equipping their laboratory. Correspondence: C. Cassagne, Laboratoire de Parasitologie-Mycologie, AP-HM Timone, 13385 Marseille CEDEX 5, France. Tel.: +33 491 38 60 90. Fax. +33 491 38 49 58. E-mail: carole.cassagne@ap-hm.fr Submitted for publication 28 October 2015 Revised 4 March 2016 Accepted for publication 12 March 2016 © 2016 Blackwell Verlag GmbH doi:10.1111/myc.12506 mycoses Diagnosis,Therapy and Prophylaxis of Fungal Diseases