Data from: Effects of sample fixation on specimen identification in biodiversity assemblies based on proteomic data (MALDI-TOF)

• Main Authors: Rossel, Sven, Martínez Arbizu, Pedro
• Format: Other/Unknown Material
• Language: unknown
• Published: Zenodo 2019
• Subjects: meiofauna; Harpacticus flexus; Harpacticoida; Ectinosomatidae spec; MALDI-TOF MS; meiobenthos; fixation; storage; Enhydrosoma propinquum; Microarthridion fallax; Copepoda; Proteome Fingerprint; Microarthridion littorale; Copepods; Harpacticus
• Online Access: https://doi.org/10.5061/dryad.1md2jq1

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. Hellinger transformed MALDI-TOF MS intensity matrix of all studied specimens The dataset contains hellinger transformed MALDI-TOF MS data measured with a Microflex LT/SH System (Bruker Daltonics) with a range from 3,000 to 15,000 m/z from 2,316 harpacticoid copepods from the North Sea (see publication for details). The rows contain the measured species. The first column contains sample names, the second column contains species names, the third column contains measurement weeks, the fourth column contains ethanol concentrations and the fifth column contains storage temperature. The remaining columns contain the 1,220 m/z values as names and the intensities as values. Effects_of_sample_fixation_for_MALDI-TOF.csv