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.