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.

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

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., ARBIZU, P. M., 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

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

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.