MALDI-TOF mass spectroscopy of yeasts and filamentous fungi for research and diagnostics in the agricultural value chain

Chemical and Biological Technologies in Agriculture

Table 1 MALDI-TOF- and DNA sequencing-based approaches complement each other

	MALDI biotyping	qRT-PCR/lamp assay	Sanger sequencing	NGS sequencing
Starting material	Crude extracts or whole cells	DNA extract from mixed sample	DNA extract from pure sample	DNA extract from community
Premises	Reference spectrum	Specific assay developed	Clone or PCR product available	None/PCR product
Equipment costs (machines)	High	Low-medium	High	High
Cost per sample	Negligible	Low-medium	Medium	High
Time for sample preparation	Short	Short-long	Long	Long
Time for analysis	Short	Medium	Medium	Medium-long
Data	Mass spectrum of one sample	Detection of one DNA fragment	DNA sequence of 400–1000 bp	In total 50 Mbp–1000 Gbp
Number of species/strains detected	Usually 1 per sample	1 per assay	1 per sample	Up to many thousands
Cultivation step required	Usually yes	No	Usually yes	No

Properties and comparison of MALDI biotyping and DNA sequencing-based approaches (of barcodes/PCR products or genomic DNA) methods for the identification of fungi. References: [100, 101]
The advantages of each method are shown in italics