1
|
Rossel S, Peters J, Charzinski N, Eichsteller A, Laakmann S, Neumann H, Martínez Arbizu P. A universal tool for marine metazoan species identification: towards best practices in proteomic fingerprinting. Sci Rep 2024; 14:1280. [PMID: 38218969 PMCID: PMC10787734 DOI: 10.1038/s41598-024-51235-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024] Open
Abstract
Proteomic fingerprinting using MALDI-TOF mass spectrometry is a well-established tool for identifying microorganisms and has shown promising results for identification of animal species, particularly disease vectors and marine organisms. And thus can be a vital tool for biodiversity assessments in ecological studies. However, few studies have tested species identification across different orders and classes. In this study, we collected data from 1246 specimens and 198 species to test species identification in a diverse dataset. We also evaluated different specimen preparation and data processing approaches for machine learning and developed a workflow to optimize classification using random forest. Our results showed high success rates of over 90%, but we also found that the size of the reference library affects classification error. Additionally, we demonstrated the ability of the method to differentiate marine cryptic-species complexes and to distinguish sexes within species.
Collapse
Affiliation(s)
- Sven Rossel
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany.
| | - Janna Peters
- German Centre for Marine Biodiversity Research (DZMB), Senckenberg am Meer, 20146, Hamburg, Germany
| | - Nele Charzinski
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Angelina Eichsteller
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| | - Silke Laakmann
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), 26129, Oldenburg, Germany
- Alfred-Wegener-Institut Helmholtz-Zentrum für Polar- und Meeresforschung, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Hermann Neumann
- Institute for Sea Fisheries, Thuenen Institute, 27572, Bremerhaven, Germany
| | - Pedro Martínez Arbizu
- Senckenberg am Meer, German Centre for Marine Biodiversity Research (DZMB), 26382, Wilhelmshaven, Germany
- Marine Biodiversity Research, Institute of Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, 26129, Oldenburg, Germany
| |
Collapse
|