Microarthridion littorale (Poppe, 1881) ist ein häufiger Vertreter der harpactioiden Copepoden (Ruderfußkrebse) in der Nordsee. Die blaue Linie entspricht dem Massenspektrum, wie es mit dem MALDI-TOF MS erzeugt wird. Besonders für solche kleinen Arten (500 – 700 µm) bietet sich die Identifikation mittels MALDI-TOF MS an, da die morphologische Identifikation sowohl schwierig, als auch zeitaufwändig ist.

Proteomic Laboratory


Species identification is a basic part of ecological and scientific studies. However, species differentiation is time-consuming and demands a comprehensive taxonomic expertise. Using proteome fingerprinting allows rapid identification even without such taxonomic knowledge. In our laboratory, we are using MALDI-TOF mass spectrometry to evaluate the proteome fingerprint.

MALDI-TOF MS means Matrix Assissted Laser Desorption/Ionization Time Of Flight Mass Spectrometry. This method uses a matrix in which analytes are embedded, which then is evaporated using a laser. Hence, analytes are set free and accelerated by an electric field through a time-of-flight tube towards a detector. Due to different time-of-flight, analytes are separated by size. Using a matrix to embed analytes, this method allows measurement of macromolecules such as peptides and proteins without destroying them due to laser radiation. The measured peptides and proteins then result in the so called proteome fingerprint. In microbiology this method is already an established identification method to differentiate bacteria, viruses or fungi. Recently, this method was also applied successfully for identification of metazoan species.

In out section we are working to prepare this method for use in biodiversity assessments where specimen identification takes most of the time within a study. That is why we are testing this method in pilot studies for a variety of animal species. Additionally to that, we are working on methods allowing rapid analyses of MALDI-TOF MS data. Using MLADI-TOF MS we aim at reducing the time necessary for species identification in biodiversity assessments. In contrast to methods such as DNA barcoding only very few preparation steps are needed from a sorted specimen to the mass spectrum used for species identification. Aside from the time saved using this method in contrast to DNA barcoding, also the costs are a lot lower, making it interesting for animal groups where lots of specimens have to be identified to species level such as meiofauna research or analyses of plankton time series. The method also allows identification of cryptic species, making it an interesting tool also for makro- or megafauna species aiding in identification of hard to discern species.

Manager

©
Viola Siegler
Dr. Sven Rossel
Leitung Proteomic Laboratory
Phone +49 4421 9475-177
sven.rossel@senckenberg.de

Link Fachbereich Proteomic Labor

Link Division Proteomic Laboratory

 

2022

Rossel, S., Uhlenkott, K., Peters, J., Vink, A., & Martínez Arbizu, P. (2022). Evaluating species richness using proteomic fingerprinting and DNA-barcoding – a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone. Marine Biodiversity.

Rossel, S., Kaiser, P., Bode-Dalby, M., Renz, J., Laakmann, S., Auel, H., Hagen, W., Arbizu, P. M., & Peters, J. (2022). Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean. Molecular Ecology Resources, n/a(n/a). https://doi.org/10.1111/1755-0998.13714

Peters, J., Laakmann, S., Rossel, S., Arbizu, P. M., & Renz, J. (2022). Perspectives of species identification by MALDI-TOF MS in monitoring—Stability of proteomic fingerprints in marine epipelagic copepods [Preprint]. Preprints. https://doi.org/10.22541/au.166671183.32080869/v1

Paulus, E., Brix, S., Siebert, A., Martínez Arbizu, P., Rossel, S., Peters, J., Svavarsson, J., & Schwentner, M. (2022). Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics. Molecular Ecology, 31(1), 313–330. https://doi.org/10.1111/mec.16234

Kürzel, K., Kaiser, S., Lörz, A.-N., Rossel, S., Paulus, E., Peters, J., Schwentner, M., Martínez Arbizu, P., Coleman, C. O., Svavarsson, J., & Brix, S. (2022). Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy. Frontiers in Marine Science, 8(795196). https://doi.org/doi: 10.3389/fmars.2021.795196

Korfhage, S. A., Rossel, S., Brix, S., McFadden, C. S., Ólafsdóttir, S. H., & Martínez Arbizu, P. (2022). Species Delimitation of Hexacorallia and Octocorallia Around Iceland Using Nuclear and Mitochondrial DNA and Proteome Fingerprinting. Frontiers in Marine Science, 9. https://www.frontiersin.org/article/10.3389/fmars.2022.838201

 

2021

Renz, J., Markhaseva, E. L., Laakmann, S., Rossel, S., Martínez Arbizu, P., & Peters, J. (2021). Proteomic fingerprinting facilitates biodiversity assessments in understudied ecosystems: A case study on integrated taxonomy of deep sea copepods. Molecular Ecology Resources.

Lins, L., Zeppilli, D., Menot, L., Michel, L. N., Bonifácio, P., Brandt, M., Pape, E., Rossel, S., Uhlenkott, K., Macheriotou, L., & others. (2021). Toward a reliable assessment of potential ecological impacts of deep-sea polymetallic nodule mining on abyssal infauna. Limnology and Oceanography: Methods.

 

2020

Rossel, S., & Martínez Arbizu, P. (2020). Unsupervised biodiversity estimation using proteomic fingerprints from MALDI-TOF MS data. Limnology and Oceanography: Methods. https://doi.org/10.1002/lom3.10358

Rossel, S., Deli, T., & Raupach, M. J. (2020). First insights into the phylogeography and demographic history of the common hermit crab Pagurus bernhardus (Linnaeus, 1758)(Decapoda: Anomura: Paguridae) across the Eastern Atlantic and North Sea. The Journal of Crustacean Biology, 40(4), 435–449.

Rossel, S., Barco, A., Kloppmann, M., Martínez Arbizu, P., Huwer, B., & Knebelsberger, T. (2020). Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS. Journal of Proteomics, 103993.

 

2019

Rossel, S., Khodami, S., & Martínez Arbizu, P. (2019). Comparison of rapid biodiversity assessment of meiobenthos using MALDI-TOF MS and Metabarcoding. Frontiers in Marine Science, 6, 659. https://doi.org/10.3389/fmars.2019.00659

Rossel, S., & Martínez Arbizu, P. (2019). Revealing higher than expected diversity of Harpacticoida (Crustacea: Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding. Scientific Reports, 9(1), 9182. https://doi.org/10.1038/s41598-019-45718-7

 

2018

Rossel, S., & Martínez Arbizu, P. (2018b). Effects of Sample Fixation on Specimen Identification in Biodiversity Assemblies based on Proteomic Data (MALDI-TOF). Frontiers in Marine Science, 5, 149. https://doi.org/10.3389/fmars.2018.00149

Rossel, S., & Martínez Arbizu, P. (2018a). Automatic specimen identification of Harpacticoids (Crustacea:Copepoda) using Random Forest and MALDI-TOF mass spectra, including a post hoc test for false positive discovery. Methods in Ecology and Evolution, 9(6), 1421–1434. https://doi.org/10.1111/2041-210X.13000

2022

18. KÜRZEL, K., KAISER, S., LÖRZ, A.-N., ROSSEL, S., PAULUS, E., PETERS, J., SCHWENTNER, M., MARTÍNEZ ARBIZU, P., COLEMAN, C. O., SVAVARSSON, J., & BRIX, S. (2022). Correct Species Identification and Its Implications for Conservation Using Haploniscidae (Crustacea, Isopoda) in Icelandic Waters as a Proxy. Frontiers in Marine Science, 8(795196). https://doi.org/doi: 10.3389/fmars.2021.795196

17. ROSSEL, S., UHLENKOTT, K., PETERS, J., VINK, A., & MARTÍNEZ ARBIZU, P. (2022). Evaluating species richness using proteomic fingerprinting and DNA-barcoding – a case study on meiobenthic copepods from the Clarion Clipperton Fracture Zone. Marine Biodiversity.

16. KORFHAGE, S. A., ROSSEL, S., BRIX, S., MCFADDEN, C. S., ÓLAFSDÓTTIR, S. H., & MARTÍNEZ ARBIZU, P.  (2022). Species Delimitation of Hexacorallia and Octocorallia Around Iceland Using Nuclear and Mitochondrial DNA and Proteome Fingerprinting. Frontiers in Marine Science, 9. https://www.frontiersin.org/article/10.3389/fmars.2022.838201

15. ROSSEL, S., KAISER, P., BODE-DALBY, M., RENZ, J., LAAKMANN, S., AUEL, H., HAGEN, W., MARTÍNEZ ARBIZU, P., & PETERS, J. (2022). Proteomic fingerprinting enables quantitative biodiversity assessments of species and ontogenetic stages in Calanus congeners (Copepoda, Crustacea) from the Arctic Ocean. Molecular Ecology Resources, n/a(n/a). https://doi.org/10.1111/1755-0998.13714

2021

14. RENZ, J., MARKHASEVA, E. L., LAAKMANN, S., ROSSEL, S., MARTÍNEZ ARBIZU, P., & PETERS, J.  (2021). Proteomic fingerprinting facilitates biodiversity assessments in understudied ecosystems: A case study on integrated taxonomy of deep sea copepods. Molecular Ecology Resources. https://doi.org/10.1111/1755-0998.13405

13. PAULUS, E., BRIX, S., SIEBERT, A., MARTÍNEZ ARBIZU, P., ROSSEL, S., PETERS, J., SVAVARSSON, J., & SCHWENTNER, M. (2022). Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics. Molecular Ecology, 31(1), 313–330. https://doi.org/10.1111/mec.16234

2020

12. ROSSEL, S., & MARTÍNEZ ARBIZU, P. (2020). Unsupervised biodiversity estimation using proteomic fingerprints from MALDI-TOF MS data. Limnology and Oceanography: Methods. https://doi.org/10.1002/lom3.10358

11. ROSSEL, S., BARCO, A., KLOPPMANN, M., MARTÍNEZ ARBIZU, P., HUWER, B., & KNEBELSBERGER, T. (2020). Rapid species level identification of fish eggs by proteome fingerprinting using MALDI-TOF MS. Journal of Proteomics, 103993. https://doi.org/10.1016/j.jprot.2020.103993

10. PETERS, J., LAAKMANN, S., ROSSEL, S., MARTÍNEZ ARBIZU, P., & RENZ, J. (2022). Perspectives of species identification by MALDI-TOF MS in monitoring—Stability of proteomic fingerprints in marine epipelagic copepods [Preprint]. Preprints. https://doi.org/10.22541/au.166671183.32080869/v1

9. WILKE, T., RENZ, J., HAUFFE, T., DELICADO, D., & PETERS, J. (2020). Proteomic Fingerprinting Discriminates Cryptic Gastropod Species. Malacologia, 63(1), 131–137. https://doi.org/10.4002/040.063.0113

2019
8. HOLST, S., HEINS, A., AND LAAKMANN, S. (2019). Morphological and molecular diagnostic species characters of Staurozoa (Cnidaria) collected on the coast of Helgoland (German Bight, North Sea). Marine Biodiversity. doi:10.1007/s12526-019-00943-1.

7. ROSSEL, S., KHODAMI, S., AND MARTÍNEZ ARBIZU, P. (2019). Comparison of rapid biodiversity assessment of meiobenthos using MALDI-TOF MS and Metabarcoding. Frontiers in Marine Science 6, 659. doi: 10.3389/fmars.2019.00659

6. ROSSEL, S., AND MARTÍNEZ ARBIZU, P. (2019). Revealing higher than expected diversity of Harpacticoida (Crustacea: Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding. Scientific Reports 9, 9182. doi: 10.1038/s41598-019-45718-7

2018
5. ROSSEL, S., AND MARTÍNEZ ARBIZU, P. (2018). Effects of Sample Fixation on Specimen Identification in Biodiversity Assemblies based on Proteomic Data (MALDI-TOF). Frontiers in Marine Science 5, 149. doi: 10.3389/fmars.2018.00149

4. ROSSEL, S., AND MARTÍNEZ ARBIZU, P. (2018). Automatic specimen identification of Harpacticoids (Crustacea: Copepoda) using Random Forest and MALDI-TOF mass spectra, including a post hoc test for false positive discovery. Methods in Ecology and Evolution 00, 1–14. doi: 10.1111/2041-210X.13000

3. KAISER, P., BODE, M., CORNILS, A., HAGEN, W., MARTÍNEZ ARBIZU, P., AUEL, H., AND LAAKMANN, S. (2018). High-resolution community analysis of deep-sea copepods using MALDI-TOF protein fingerprinting. Deep Sea Research Part I: Oceanographic Research Papers. doi:10.1093/plankt/fbx031

2017
2. BODE, M., LAAKMANN, S., KAISER, P., HAGEN, W., AUEL, H., AND CORNILS, A. (2017). Unravelling diversity of deep-sea copepods using integrated morphological and molecular techniques. Journal of Plankton Research 39, 600–617. doi: 10.1016/j.dsr.2018.06.005

2013
1. LAAKMANN, S., GERDTS, G., ERLER, R., KNEBELSBERGER, T., MARTÍNEZ ARBIZU, P., AND RAUPACH, M. J. (2013). Comparison of molecular species identification for North Sea calanoid copepods (Crustacea) using proteome fingerprints and DNA sequences. Mol Ecol Resour 13, 862–76. doi:10.1111/1755-0998.12139.

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