Publications
Acknowledged contributions
The DTU Proteomics Core facility supports a wide range of research by providing access to advanced mass spectrometry and proteomics expertise. We work closely with researchers throughout the process, from sample preparation to data analysis, helping turn complex biological questions into meaningful results. The publications below highlight studies where our contributions have supported new insights and practical applications of proteomics in research.
| Title | Link | |
|---|---|---|
| 1 | Reverenna, M., Nielsen, M. W., Wolff, D. S., Daniel, J., Lytra, E., Thumtecho, S., Colaianni, P. D., Ljungars, A., Laustsen, A. H., Schoof, E. M., Van Goey, J., Jenkins, T. P., Lukassen, M. V., Santos, A., & Kalogeropoulos, K. (2026). Generalizable Direct Protein Sequencing With InstaNexus. Molecular & cellular proteomics : MCP, 25(4), 101547. | https://doi.org/10.1016/j.mcpro.2026.101547 |
| 2 | Amador, C. I., Moscovitz, S. Z., Maccario, L., Herschend, J., Kramer, I., Jeckel, H., Cooper, V. S., Drescher, K., Neu, T. R., Burmølle, M., & Røder, H. L. (2025). Evolution of genotypic and phenotypic diversity in multispecies biofilms. NPJ biofilms and microbiomes, 11(1), 118. | https://doi.org/10.1038/s41522-025-00755-1 |
| 3 | Wagner, M., Kang, J., Mercado, C., Thirumlaikumar, V. P., Gorka, M., Zillmer, H., Guo, J., Minen, R. I., Plecki, C. F., Dehesh, K., Schroeder, F. C., Walther, D., & Skirycz, A. (2025). Mapping protein-metabolite interactions in E. coli by integrating chromatographic techniques and co-fractionation mass spectrometry. iScience, 28(6), 112611. | https://doi.org/10.1016/j.isci.2025.112611 |
| 4 | García-Blay, Ó., & Hansen, M. M. K. (2025). Protocol to identify proteins as regulators of gene expression noise. STAR protocols, 6(2), 103763. | https://doi.org/10.1016/j.xpro.2025.103763 |
| 5 | Amador, C. I., Røder, H. L., Herschend, J., Neu, T. R., & Burmølle, M. (2025). Decoding the impact of interspecies interactions on biofilm matrix components. Biofilm, 9, 100271. | https://doi.org/10.1016/j.bioflm.2025.100271 |
| 6 | Farias, P., Francisco, R., Maccario, L., Herschend, J., Sørensen, S. J., & Morais, P. V. (2025). Metabolic response of tellurite resistant Bacillus altitudinis strain 3W19 highlights the potential as a model organism for bioremediation. Scientific reports, 15(1), 12745. | https://doi.org/10.1038/s41598-025-95321-2 |
| 7 | Eloff, K., Kalogeropoulos, K., Mabona, A., Morell, O., Catzel, R., Rivera-de-Torre, E., Jespersen, J. B., Williams, W., van Beljouw, S. P. B., Skwark, M. J., Laustsen, A. H., Brouns, S. J. J., Ljungars, A., Schoof, E. M., Van Goey, J., Keller, U. A. d., Beguir, K., Carranza, N. L., & Jenkins, T. P. (2025). InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments. Nature machine intelligence, 7(4), 565-579. | https://doi.org/10.1038/s42256-025-01019-5 |
| 8 | Ahmadi, S., Burlet, N. J., Benard-Valle, M., Guadarrama-Martínez, A., Kerwin, S., Cardoso, I. A., Marriott, A. E., Edge, R. J., Crittenden, E., Neri-Castro, E., Fernandez-Quintero, M. L., Nguyen, G. T. T., O'Brien, C., Wouters, Y., Kalogeropoulos, K., Thumtecho, S., Ebersole, T. W., Dahl, C. H., Glegg-Sørensen, E. U., ... & Laustsen, A. H. (2025). Nanobody-based recombinant antivenom for cobra, mamba and rinkhals bites. Nature, 647(8090), 716-725. | https://doi.org/10.1038/s41586-025-09661-0 |
| 9 | Kastberg, L. L. B., Jacobsen, I. H., Özdemir, E., Workman, C. T., Jensen, M. K., & Förster, J. (2025). Characterizing heterologous protein burden in Komagataella phaffii. FEMS yeast research, 25, foaf007. | https://doi.org/10.1093/femsyr/foaf007 |
| 10 | Reverenna, M., Wennekers Nielsen, M., Wolff, D. S., Lytra, E., Colaianni, P., Ljungars, A., Laustsen, A., Schoof, E., Van Goey, J., Jenkins, T., Lukassen, M., Santos, A., & Kalogeropoulos, K. (2025). Generalizable direct protein sequencing with InstaNexus. bioRxiv. | https://doi.org/10.1101/2025.07.25.666861 |
| 11 | Lauridsen, J., Ramasamy, P., Catzel, R., Canbay, V., Mabona, A., Eloff, K., Fullwood, P., Ferguson, J., Kirketerp-Møller, A., Goldschmidt, I. S., Claeys, T., van Puyenbroeck, S., Lopez Carranza, N., Schoof, E., Martens, L., Van Goey, J., Francavilla, C., Jenkins, T. P., & Kalogeropoulos, K. (2025). InstaNovo-P: A de novo peptide sequencing model for phosphoproteomics. bioRxiv. | https://doi.org/10.1101/2025.05.14.654049 |
| 12 | Rappold, R., Kalogeropoulos, K., La Regina, G., Auf dem Keller, U., Slack, E., & Vogel, V. (2025). Relaxation of mucosal fibronectin fibers in late gut inflammation following neutrophil infiltration in mice. npj biological physics and mechanics, 2(1), 4. | https://doi.org/10.1038/s44341-024-00006-y |
| 13 | Kalogeropoulos, K., Moldt Haack, A., Madzharova, E., Di Lorenzo, A., Hanna, R., Schoof, E. M., & Auf dem Keller, U. (2024). CLIPPER 2.0: Peptide-Level Annotation and Data Analysis for Positional Proteomics. Molecular & cellular proteomics : MCP, 23(6), 100781. | https://doi.org/10.1016/j.mcpro.2024.100781 |
| 14 | Nørregaard, K. S., Jürgensen, H. J., Heltberg, S. S., Gårdsvoll, H., Bugge, T. H., Schoof, E. M., Engelholm, L. H., & Behrendt, N. (2024). A proteomics-based survey reveals thrombospondin-4 as a ligand regulated by the mannose receptor in the injured lung. The Journal of biological chemistry, 300(5), 107284. | https://doi.org/10.1016/j.jbc.2024.107284 |
| 15 | Meliawati, M., Volke, D. C., Nikel, P. I., & Schmid, J. (2024). Engineering the carbon and redox metabolism of Paenibacillus polymyxa for efficient isobutanol production. Microbial biotechnology, 17(3), e14438. | https://doi.org/10.1111/1751-7915.14438 |
| 16 | Cai, J., Nielsen, M. W., Kalogeropoulos, K., Auf dem Keller, U., & van der Plas, M. J. A. (2024). Peptidomic analysis of endogenous and bacterial protease activity in human plasma and wound fluids. iScience, 27(2), 109005. | https://doi.org/10.1016/j.isci.2024.109005 |
| 17 | Neil, C., Newman, J., Stonehouse, N. J., Rowlands, D. J., Belsham, G. J., & Tuthill, T. J. (2024). The pseudoknot region and poly-(C) tract comprise an essential RNA packaging signal for assembly of foot-and-mouth disease virus. PLoS pathogens, 20(12), e1012283. | https://doi.org/10.1371/journal.ppat.1012283 |
| 18 | de Figueiredo, F. L., Contesini, F. J., Terrasan, C. R. F., Gerhardt, J. A., Corrêa, A. B., Antoniel, E. P., Wassano, N. S., Levassor, L., Rabelo, S. C., Franco, T. T., Mortensen, U. H., & Damasio, A. (2024). Engineering the secretome of Aspergillus niger for cellooligosaccharides production from plant biomass. Microbial cell factories, 23(1), 323. | https://doi.org/10.1186/s12934-024-02578-9 |
| 19 | Røder, H. L., Christidi, E., Amador, C. I., Music, S., Olesen, A. K., Svensson, B., Madsen, J. S., Herschend, J., Kreft, J., & Burmølle, M. (2024). Flagellar interference with plasmid uptake in biofilms: a joint experimental and modeling study. Applied and environmental microbiology, 90(1), e0151023. | https://doi.org/10.1128/aem.01510-23 |
| 20 | Petrosius, V., Aragon-Fernandez, P., Üresin, N., Kovacs, G., Phlairaharn, T., Furtwängler, B., Op De Beeck, J., Skovbakke, S. L., Goletz, S., Thomsen, S. F., Keller, U. A. d., Natarajan, K. N., Porse, B. T., & Schoof, E. M. (2023). Exploration of cell state heterogeneity using single-cell proteomics through sensitivity-tailored data-independent acquisition. Nature communications, 14(1), 5910. | https://doi.org/10.1038/s41467-023-41602-1 |
| 21 | Kristensen, S. S., Lukassen, M. V., Siebenhaar, S., Diep, D. B., Morth, J. P., & Mathiesen, G. (2023). Lactiplantibacillus plantarum as a novel platform for production and purification of integral membrane proteins using RseP as the benchmark. Scientific reports, 13(1), 14361. | https://doi.org/10.1038/s41598-023-41559-7 |
| 22 | Lindqvist, L. L., Jarmusch, S. A., Sonnenschein, E. C., Strube, M. L., Kim, J., Nielsen, M. W., Kempen, P. J., Schoof, E. M., Zhang, S., & Gram, L. (2023). Tropodithietic Acid, a Multifunctional Antimicrobial, Facilitates Adaption and Colonization of the Producer, Phaeobacter piscinae. mSphere, 8(1), e0051722. | https://doi.org/10.1128/msphere.00517-22 |
| 23 | Tresse, E., Marturia-Navarro, J., Sew, W. Q. G., Cisquella-Serra, M., Jaberi, E., Riera-Ponsati, L., Fauerby, N., Hu, E., Kretz, O., Aznar, S., & Issazadeh-Navikas, S. (2023). Mitochondrial DNA damage triggers spread of Parkinson's disease-like pathology. Molecular psychiatry, 28(11), 4902-4914. | https://doi.org/10.1038/s41380-023-02251-4 |
| 24 | Rønne, M. E., Tandrup, T., Madsen, M., Hunt, C. J., Myers, P. N., Moll, J. M., Holck, J., Brix, S., Strube, M. L., Aachmann, F. L., Wilkens, C., & Svensson, B. (2023). Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate. Applied and environmental microbiology, 89(10), e0118523. | https://doi.org/10.1128/aem.01185-23 |
| 25 | Rappold, R., Kalogeropoulos, K., auf dem Keller, U., Vogel, V., & Slack, E. (2023). Salmonella-driven Intestinal Edema in Mice is Characterized by Tensed Fibronectin Fibers. bioRxiv. | https://doi.org/10.1101/2023.07.26.550515 |
| 26 | Gnosa, S. P., Puig Blasco, L., Piotrowski, K. B., Freiberg, M. L., Savickas, S., Madsen, D. H., Auf dem Keller, U., Kronqvist, P., & Kveiborg, M. (2022). ADAM17-mediated EGFR ligand shedding directs macrophage-promoted cancer cell invasion. JCI insight, 7(18), e155296. | https://doi.org/10.1172/jci.insight.155296 |
| 27 | Zhang, S., Lindqvist, L. L., Isbrandt, T., Borre, I. L., Wibowo, M., Nielsen, M. W., Ding, L., Larsen, T. O., & Gram, L. (2022). Solonamides, a Group of Cyclodepsipeptides, Influence Motility in the Native Producer Photobacterium galatheae S2753. Applied and environmental microbiology, 88(17), e0110522. | https://doi.org/10.1128/aem.01105-22 |
| 28 | Hartmann, F. S. F., Weiß, T., Shen, J., Smahajcsik, D., Savickas, S., & Seibold, G. M. (2022). Visualizing the pH in Escherichia coli Colonies via the Sensor Protein mCherryEA Allows High-Throughput Screening of Mutant Libraries. mSystems, 7(3), e0021922. | https://doi.org/10.1128/msystems.00219-22 |
| 29 | Fiil, B. K., Thrane, S. W., Pichler, M., Kittilä, T., Ledsgaard, L., Ahmadi, S., Hermansen, G. M. M., Jelsbak, L., Lauridsen, C., Brix, S., & Laustsen, A. H. (2022). Orally active bivalent VHH construct prevents proliferation of F4+ enterotoxigenic Escherichia coli in weaned piglets. iScience, 25(4), 104003. | https://doi.org/10.1016/j.isci.2022.104003 |
| 30 | Furtwängler, B., Üresin, N., Motamedchaboki, K., Huguet, R., Lopez-Ferrer, D., Zabrouskov, V., Porse, B. T., & Schoof, E. M. (2022). Real-Time Search-Assisted Acquisition on a Tribrid Mass Spectrometer Improves Coverage in Multiplexed Single-Cell Proteomics. Molecular & cellular proteomics : MCP, 21(4), 100219. | https://doi.org/10.1016/j.mcpro.2022.100219 |
| 31 | Navarrete, C., Sánchez, B. J., Savickas, S., & Martínez, J. L. (2022). DebaryOmics: an integrative -omics study to understand the halophilic behaviour of Debaryomyces hansenii. Microbial biotechnology, 15(4), 1133-1151. | https://doi.org/10.1111/1751-7915.13954 |
| 32 | Mikosiński, J., Kalogeropoulos, K., Bundgaard, L., Larsen, C. A., Savickas, S., Moldt Haack, A., Pańczak, K., Rybołowicz, K., Grzela, T., Olszewski, M., Ciszewski, P., Sitek-Ziółkowska, K., Twardowska-Saucha, K., Karczewski, M., Rabczenko, D., Segiet, A., Buczak-Kula, P., Schoof, E. M., Eming, S. A., ... & Auf dem Keller, U. (2022). Longitudinal Evaluation of Biomarkers in Wound Fluids from Venous Leg Ulcers and Split-thickness Skin Graft Donor Site Wounds Treated with a Protease-modulating Wound Dressing. Acta dermato-venereologica, 102, adv00834. | https://doi.org/10.2340/actadv.v102.325 |
| 33 | Nguyen, G. T. T., O'Brien, C., Wouters, Y., Seneci, L., Gallissà-Calzado, A., Campos-Pinto, I., Ahmadi, S., Laustsen, A. H., & Ljungars, A. (2022). High-throughput proteomics and in vitro functional characterization of the 26 medically most important elapids and vipers from sub-Saharan Africa. GigaScience, 11, giac121. | https://doi.org/10.1093/gigascience/giac121 |
| 34 | Madsen, M., Khan, S., Kunstmann, S., Aachmann, F. L., Ipsen, R., Westh, P., Emanuelsson, C., & Svensson, B. (2022). Unaided efficient transglutaminase cross-linking of whey proteins strongly impacts the formation and structure of protein alginate particles. Food chemistry. Molecular sciences, 5, 100137. | https://doi.org/10.1016/j.fochms.2022.100137 |
| 35 | Farias, P., Francisco, R., Maccario, L., Herschend, J., Piedade, A. P., Sørensen, S., & Morais, P. V. (2021). Impact of Tellurite on the Metabolism of Paenibacillus pabuli AL109b With Flagellin Production Explaining High Reduction Capacity. Frontiers in microbiology, 12, 718963. | https://doi.org/10.3389/fmicb.2021.718963 |
| 36 | Yu, R., Campbell, K., Pereira, R., Björkeroth, J., Qi, Q., Vorontsov, E., Sihlbom, C., & Nielsen, J. (2020). Nitrogen limitation reveals large reserves in metabolic and translational capacities of yeast. Nature communications, 11(1), 1881. | https://doi.org/10.1038/s41467-020-15749-0 |
| 37 | Johansson, H. K. L., Svingen, T., Boberg, J., Fowler, P. A., Stead, D., Vinggaard, A. M., & Filis, P. (2020). Calretinin is a novel candidate marker for adverse ovarian effects of early life exposure to mixtures of endocrine disruptors in the rat. Archives of toxicology, 94(4), 1241-1250. | https://doi.org/10.1007/s00204-020-02697-3 |
| 38 | Yeung, C. C., Schoof, E. M., Tamáš, M., Mackey, A. L., & Kjaer, M. (2020). Proteomics identifies differences in fibrotic potential of extracellular vesicles from human tendon and muscle fibroblasts. Cell communication and signaling : CCS, 18(1), 177. | https://doi.org/10.1186/s12964-020-00669-9 |
| 39 | Nasipuri, P., Herschend, J., Brejnrod, A. D., Madsen, J. S., Espersen, R., Svensson, B., Burmølle, M., Jacquiod, S., & Sørensen, S. J. (2020). Community-intrinsic properties enhance keratin degradation from bacterial consortia. PloS one, 15(1), e0228108. | https://doi.org/10.1371/journal.pone.0228108 |
DTU Proteomics Core publications
The publications below include work authored by members of the DTU Proteomics Core facility. Alongside supporting research, the core team is actively engaged in scientific work and contributes directly to publications. The list is divided into publications from current core members and the full publication record, reflecting both ongoing activity and contributions over time.
