Abstract
Recently, MALDI-TOF mass spectrometry has been used to reliably identify taxonomically difficult harpacticoid copepods from sediment samples. In agreement with former studies, a negative impact of short storage periods was stated. Other studies reported inferior mass spectra quality from samples fixated in varying ethanol concentrations. Therefore, sediment samples from a mudflat sampling site in the North Sea were stored under different temperature conditions to explore a possible storage effect. Samples were fixated with either 70% or 100% ethanol and specimens were measured using MALDI-TOF mass spectrometry after one, two, three, five, seven and 12 weeks. The changes in number of peaks per species and the ability to identify specimens based on mass spectra were analyzed quality measurements. We show that storage temperature had a major impact on data quality, as for some species a loss of up to 50% of mass peaks and an increase of failed measurements to over 70% was observed. However, the effect of different ethanol concentrations on data quality was negligible. Concluding from these results, storage of metazoan samples in general and, particularly, of sediment samples at low temperatures of around -25°C is recommended to receive high-quality mass spectra for specimen identification.
Highlights
Due to their small size, enormous abundances, and high diversity (Coull et al, 1977), species identification of harpacticoid copepods is very difficult and time-consuming
Further 39 (1.68%) specimens were used for simultaneous MALDI-TOF MS analysis and amplification of the c oxidase subunit I (COI) barcode fragment
A Random Forest (RF) model based on these 200 specimens resulted in a class error of 0 for all species
Summary
Due to their small size, enormous abundances, and high diversity (Coull et al, 1977), species identification of harpacticoid copepods is very difficult and time-consuming. Most studies do not focus only on single sampling sites but on various sites with several sample replicates. They demand the identification of several 1,000 specimens and a rapid and reliable, yet cost-efficient, species identification method would be a great advantage for meiofaunal research. DNA barcoding, using a fragment of cytochrome c oxidase subunit I (COI) was introduced (Hebert et al, 2003a,b) and found wide application for specimen identification.
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