Identification of freshwater zooplankton species using protein profiling and principal component analysis

Crustaceans are vital components of the freshwater zooplankton that link various trophic levels. Because crustaceans, particularly cladocerans of the Daphnia genus, are sensitive to environmental changes, they can serve as indicators of environmental fluctuations. Therefore, it is highly desirable to have a fast and reliable method for the identification of individual Daphnia species. In this study, we demonstrated the ability of protein profiling to distinguish between freshwater zooplankton species. Individual specimens were morphologically identified before being analyzed by proteomic fingerprinting using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS). The obtained mass spectra were used to create a reference library. Subsequently, the individual species were successfully identified using Biotyper software. The variability between the spectra of individual Daphnia species was verified by principal component analysis (PCA). Our results suggest that the combination of proteome fingerprinting using MALDI-TOF MS and PCA has considerable potential as a rapid tool for the unambiguous identification of individual species of freshwater zooplankton without the need for expert morphological analysis.