Data from: Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean

Species identification is pivotal in biodiversity assessments, and
proteomic fingerprinting by MALDI-TOF mass spectrometry has already been
shown to reliably identify calanoid copepods to species level. However,
MALDI-TOF data may contain more information beyond mere species
identification. In this study, we investigated different ontogenetic
stages (copepodids C1-C6 females) of three co-occurring Calanus species
from the Arctic Fram Strait, which cannot be identified to species level
based on morphological characters alone. Differentiation of the three
species based on mass spectrometry data was without any error. In
addition, a clear stage-specific signal was detected in all species,
supported by clustering approaches as well as machine learning using
Random Forest. More complex mass spectra in later ontogenetic stages as
well as relative intensities of certain mass peaks were found as the main
drivers of stage distinction in these species. Through a dilution series,
we were able to show that this did not result from the higher amount of
biomass that was used in tissue processing of the larger stages. Finally,
the data were tested in a simulation for application in a real
biodiversity assessment by using Random Forest for stage classification of
specimens absent from the training data. This resulted in a successful
stage-identification rate of almost 90%, making proteomic fingerprinting a
promising tool to investigate polewards shifts of Atlantic Calanus species
and, in general, to assess stage compositions in biodiversity assessments
of Calanoida, which can be notoriously difficult using conventional
identification methods.