Perspectives of proteomic fingerprinting for marine zooplankton
monitoring studies
Despite the extensive use of MALDI-TOF for pathogen screening in
medicine (Croxatto et al. 2012), the method has, to our best knowledge,
not found its way into any standard protocols in metazoan monitoring.
Proteomic fingerprinting has been successfully used in pioneer survey
studies on insects, specifically vectors, proving its general value for
monitoring (Müller et al., 2020). Yet, it is still far from being an
established and validated method in biodiversity assessments or
time-series approaches. All recent findings on metazoans promise great
potential, and proteomic fingerprinting has several advantages that
argue for its own role in species identification. Sample processing is
quite easy, fast and cost-efficient (Rossel et al., 2019) and
measurement success rates are extremely high (Renz et al., 2021), if
sample quality is sufficient (Rossel & Martinez Arbizu, 2018b, Rossel
et al., 2021). These properties make the method a potential gap filler
in marine monitoring approaches despite the rapidly evolving use of
single and multi-species genetic methods. Standard morphological
identification and counting procedures in zooplankton monitoring would
not need to be changed as the approach is not intended to replace
established routines
but
to provide additional rapid in-depth taxonomic resolution of specimens
where needed. Formalin sampling becomes more and more replaced or
supplemented by alcohol sampling in marine zooplankton research, opening
the floor for many molecular approaches to add to classical counting,
including proteomics. Bearing an additional physiological signature the
fingerprint may provide information beyond pure species name, e.g. on
developmental stage (Laakmann et al., 2013, Rossel et al., accepted),
gender (Lafri et al., 2016), environmental conditions (Karger et al.,
2013) or feeding status (Niare et al., 2017, Tandina et al., 2018,
Hlavackova et al., 2019). Successful detection of microplastics by
MALDI-TOF MS (Adhikari et al., 2022) may even open future options for
simultaneous detection of contamination. However, the method is still in
its infancy, proteomic barcodes need to be established for most marine
taxa, species delimitation models are under development and collateral
information of proteomic signals still needs to be deciphered. Our
understanding for marker variability is growing, for marine copepods we
showed here that due to regional variability a construction of local
databases covering seasonal variability is strongly recommended. Impacts
of library composition need to be thoroughly tested. The establishment
of curated, freely accessible databases, accompanied by the development
of standardized data processing steps and adapted classification
algorithms, will be a fundamental step in elevating the method from an
experimental state to an applied standard procedure in marine science.