Perspectives of species identification by MALDI-TOF MS in monitoring -
stability of proteomic fingerprints in marine epipelagic copepods
Abstract
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
rather based on complex pattern-differences than on presence of single
markers. Proteomic distance was not consistently related to phylogenetic
distance. A species-gap in proteome composition appeared at 0.8
Euclidean distance when using only specimens from the same sample. When
other regions or seasons were included, intra-specific variability
increased, resulting in overlaps of intra- and inter-specific distance.
Highest intra-specific distances (> 0.8) were observed
between specimens from brackish and marine habitats i.e., salinity
likely affects proteomic patterns. When testing library sensitivity of
the RF model to regionality, strong misidentification was only detected
between two congener pairs. Still, choice of reference library may have
an impact on identification of closely related species and should be
tested before routine application. We envision high relevance of this
time- and cost-efficient method for future zooplankton monitoring as it
provides not only in-depth taxonomic resolution for counted specimens
but also add-on information e.g., on developmental stage or
environmental conditions.