Proteomic spectra of epipelagic copepods

We analyzed robustness of species identification based on proteomic composition to data processing and intraspecific variability, specificity and sensitivity of species-markers as well as discriminatory power of proteomic fingerprinting and its sensitivity to phylogenetic distance. Our analysis is based on MALDI-TOF MS data from 32 marine copepod species coming from 13 regions (North and Central Atlantic and adjacent seas). A random forest (RF) model correctly classified all specimens to species level with only small sensitivity to data processing, demonstrating the strong robustness of the method. Compounds with high specificity showed low sensitivity i.e., identification was based on complex pattern-differences rather than on presence of single markers., Specimens were derived from ethanol samples (> 96 %), which were collected during diverse monitoring programs or field campaigns and from a copepod culture. Age and storing conditions varied between samples, samples were stored at 4°C from 2018 onwards. Adult female copepods were identified morphologically to species level and stored in ethanol until further processing at 4°C. In total, 752 specimens from 32 species, and 13 different regions were used for proteomic fingerprinting analyses. Proteomic profiles were determined for all 752 specimens. For small copepods (< 2 mm), the whole specimen, and for larger copepods, a piece of the cephalosome was shortly dried at room temperature and kept in an Eppendorf tube. Depending on sample size 5–10 µl matrix solution (α-Cyano-4-hydroxycinnamic acid as saturated solution in 50% acetonitrile, 47.5% LC-MS grade water, and 2.5% trifluoroacetic acid) was added. After at least 10 min extraction, 1.2 µl of each sample was added onto the target...,