MALDI-TOF MS technique as a new approach for simultaneous detection and differentiation of potato virus Y strains

Due to high variability, potato virus Y (PVY) is an excellent model for developing new virus detection and strain differentiation methods. We present a pioneering assessment using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) to identify three predominant strains of PVY: PVY^O, PVY^NTN, and PVY^N-Wi. We prepared and characterized the genomic, protein, and whole-virus samples. MALDI analysis yielded distinct spectral signatures for each strain, enabling identification. The protein extracts analyzed in the LP 2-20 kDa mode showed the highest spectral richness for N-Wi and O strains, with significant statistical differentiation (p < 0.05) across specific m/z values. RT-qPCR linear detection ranged from 6000 to 0.6 pg of viral RNA. MALDI-TOF MS identified the PVY strains down to 0.001 mg/mL. The Principal Component Analysis outcomes highlighted the distinct clustering of PVY strains based on their MALDI-TOF spectra, with a 45% laser power setting emerging as optimal for balancing the spectral quality across strains. Mann-Whitney U-test comparisons of ion intensity distributions reinforced MALDI's discriminative accuracy, revealing statistically significant (p < 0.05) ion signals unique to each strain. Our study steps forward in applying MALDI-TOF MS for simultaneous viral strain detection and identification.