Back to Senior Research Scientists
Ulrike Kusebauch

Ulrike Kusebauch, PhD

Senior Research Scientist

Moritz Lab

Send Email
  • Biography
  • Expertise
  • Publications

Dr. Kusebauch’s research activities include the development and application of proteomic technologies, with a particular focus on targeted proteomics in biomedical research. Dr. Kusebauch studied Pharmaceutical Chemistry and obtained her Ph.D. in Biochemistry at the Max Planck Institute of Biochemistry (Germany) focusing on peptide/organic chemistry and conformational studies at temporal resolution. For her postdoctoral work, she joined the group of Prof. Ruedi Aebersold where she contributed to the development of targeted proteomics by selected reaction monitoring (SRM).

Dr. Kusebauch continued her research at ISB where she developed complete proteome SRM and SWATH mass spectrometry resources for human and other organisms, e.g., the Human SRMAtlas (www.srmatlas.org), a public available resource of targeted assays to quantify any protein in the human proteome, and applies quantitative technologies to spatial and temporal proteome dynamics and biochemical mechanisms in infectious and chronic human diseases. Other work includes the discovery of tyrosine phosphorylation in Mycobacterium tuberculosis revealing a previously unrecognized post-translational modification system in a human pathogen that claims ∼1.4 million lives every year. Dr. Kusebauch received the Human Proteome Organization Discovery in Proteomics Sciences Award 2018 that recognizes the outstanding efforts and achievements of individuals in the field of proteomics.

Proteomics, Mass Spectrometry, Post-translational Modification (PTM’s), Protein Biochemistry, Systems Biology, Peptide Chemistry, Pharmaceutical Chemistry
Kusebauch, Ulrike, Alan P. R. Lorenzetti, David S. Campbell, Min Pan, David Shteynberg, Charu Kapil, Mukul K. Midha, Adrián López García de Lomana, Nitin S. Baliga, and Robert L. Moritz. 2023. “A Comprehensive Spectral Assay Library to Quantify the Halobacterium Salinarum NRC-1 Proteome by DIA/SWATH-MS.” Scientific Data 10 (1): 697. https://doi.org/10.1038/s41597-023-02590-5. Cite Download
Burns, Adam R., Jack Wiedrick, Alicia Feryn, Michal Maes, Mukul K. Midha, David H. Baxter, Seamus R. Morrone, et al. 2023. “Proteomic Changes Induced by Longevity-Promoting Interventions in Mice.” GeroScience. https://doi.org/10.1007/s11357-023-00917-z. Cite
Watanabe, Kengo, Tomasz Wilmanski, Priyanka Baloni, Max Robinson, Gonzalo G. Garcia, Michael R. Hoopmann, Mukul K. Midha, et al. 2023. “Lifespan-Extending Interventions Induce Consistent Patterns of Fatty Acid Oxidation in Mouse Livers.” Communications Biology 6 (1): 768. https://doi.org/10.1038/s42003-023-05128-y. Cite
Morrone, Seamus R., Michael R. Hoopmann, David D. Shteynberg, Ulrike Kusebauch, and Robert L. Moritz. 2023. “Optimization of Instrument Parameters for Efficient Phosphopeptide Identification and Localization by Data-Dependent Analysis Using Orbitrap Tribrid Mass Spectrometers.” ChemRxiv. https://doi.org/10.26434/chemrxiv-2023-qklh1-v2. Cite Download
Lorenzetti, Alan P. R., Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L G de Lomana, et al. 2023. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” MSystems, e0081622. https://doi.org/10.1128/msystems.00816-22. Cite Download
Lorenzetti, Alan P. R., Ulrike Kusebauch, Lívia S. Zaramela, Wei-Ju Wu, João P. P. de Almeida, Serdar Turkarslan, Adrián L. G. de Lomana, et al. 2022. “A Genome-Scale Atlas Reveals Complex Interplay of Transcription and Translation in an Archaeon.” bioRxiv. https://doi.org/10.1101/2022.08.31.505529. Cite Download
Watanabe, Kengo, Tomasz Wilmanski, Priyanka Baloni, Max Robinson, Gonzalo G. Garcia, Michael R. Hoopmann, Mukul K. Midha, et al. 2022. “Systems-Level Patterns in Biological Processes Are Changed under Prolongevity Interventions and across Biological Age.” medRxiv. https://doi.org/10.1101/2022.07.11.22277435. Cite Download
Martyn, Gregory D., Gianluca Veggiani, Ulrike Kusebauch, Seamus R. Morrone, Bradley P. Yates, Alex U. Singer, Jiefei Tong, et al. 2022. “Engineered SH2 Domains for Targeted Phosphoproteomics.” ACS Chemical Biology 17 (6): 1472–84. https://doi.org/10.1021/acschembio.2c00051. Cite
Maixner, Frank, Mohamed S. Sarhan, Kun D. Huang, Adrian Tett, Alexander Schoenafinger, Stefania Zingale, Aitor Blanco-Míguez, et al. 2021. “Hallstatt Miners Consumed Blue Cheese and Beer during the Iron Age and Retained a Non-Westernized Gut Microbiome until the Baroque Period.” Current Biology: CB, S0960-9822(21)01271-9. https://doi.org/10.1016/j.cub.2021.09.031. Cite Download
Kumar, Sudhir, Meseret T. Haile, Michael R. Hoopmann, Linh T. Tran, Samantha A. Michaels, Seamus R. Morrone, Kayode K. Ojo, et al. 2021. “Plasmodium Falciparum Calcium-Dependent Protein Kinase 4 Is Critical for Male Gametogenesis and Transmission to the Mosquito Vector.” MBio, e0257521. https://doi.org/10.1128/mBio.02575-21. Cite
Diener, Christian, Anna C. H. Hoge, Sean M. Kearney, Ulrike Kusebauch, Sushmita Patwardhan, Robert L. Moritz, Susan E. Erdman, and Sean M. Gibbons. 2021. “Non-Responder Phenotype Reveals Apparent Microbiome-Wide Antibiotic Tolerance in the Murine Gut.” Communications Biology 4 (1): 316. https://doi.org/10.1038/s42003-021-01841-8. Cite Download
López García de Lomana, Adrián, Ulrike Kusebauch, Arjun V. Raman, Min Pan, Serdar Turkarslan, Alan P. R. Lorenzetti, Robert L. Moritz, and Nitin S. Baliga. 2020. “Selective Translation of Low Abundance and Upregulated Transcripts in Halobacterium Salinarum.” MSystems 5 (4). https://doi.org/10.1128/mSystems.00329-20. Cite Download
Adhikari, Subash, Edouard C. Nice, Eric W. Deutsch, Lydie Lane, Gilbert S. Omenn, Stephen R. Pennington, Young-Ki Paik, et al. 2020. “A High-Stringency Blueprint of the Human Proteome.” Nature Communications 11 (1): 5301. https://doi.org/10.1038/s41467-020-19045-9. Cite Download
Hoopmann, Michael R., Ulrike Kusebauch, Magnus Palmblad, Nuno Bandeira, David D. Shteynberg, Lingjie He, Bin Xia, et al. 2020. “Insights from the First Phosphopeptide Challenge of the MS Resource Pillar of the HUPO Human Proteome Project.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.0c00648. Cite
Midha, Mukul K., Ulrike Kusebauch, David Shteynberg, Charu Kapil, Samuel L. Bader, Panga Jaipal Reddy, David S. Campbell, Nitin S. Baliga, and Robert L. Moritz. 2020. “A Comprehensive Spectral Assay Library to Quantify the Escherichia Coli Proteome by DIA/SWATH-MS.” Scientific Data 7 (1): 389. https://doi.org/10.1038/s41597-020-00724-7. Cite
Midha, Mukul K., David S. Campbell, Charu Kapil, Ulrike Kusebauch, Michael R. Hoopmann, Samuel L. Bader, and Robert L. Moritz. 2020. “DIALib-QC an Assessment Tool for Spectral Libraries in Data-Independent Acquisition Proteomics.” Nature Communications 11 (1): 5251. https://doi.org/10.1038/s41467-020-18901-y. Cite Download
Herrmann, Marietta, Anne Babler, Irina Moshkova, Felix Gremse, Fabian Kiessling, Ulrike Kusebauch, Valentin Nelea, et al. 2020. “Lumenal Calcification and Microvasculopathy in Fetuin-A-Deficient Mice Lead to Multiple Organ Morbidity.” PloS One 15 (2): e0228503. https://doi.org/10.1371/journal.pone.0228503. Cite Download
Shteynberg, David D., Eric W. Deutsch, David S. Campbell, Michael R. Hoopmann, Ulrike Kusebauch, Dave Lee, Luis Mendoza, et al. 2019. “PTMProphet: Fast and Accurate Mass Modification Localization for the Trans-Proteomic Pipeline.” BioRxiv, 679845. https://doi.org/10.1101/679845. Cite Download
Maixner, Frank, Dmitrij Turaev, Amaury Cazenave-Gassiot, Marek Janko, Ben Krause-Kyora, Michael R. Hoopmann, Ulrike Kusebauch, et al. 2018. “The Iceman’s Last Meal Consisted of Fat, Wild Meat, and Cereals.” Current Biology: CB. https://doi.org/10.1016/j.cub.2018.05.067. Cite
Kusebauch, Ulrike, Lorenzo E. Hernández-Castellano, Stine L. Bislev, Robert L. Moritz, Christine M. Røntved, and Emøke Bendixen. 2018. “Selected Reaction Monitoring Mass Spectrometry of Mastitis Milk Reveals Pathogen-Specific Regulation of Bovine Host Response Proteins.” Journal of Dairy Science. https://doi.org/10.3168/jds.2017-14312. Cite
Michalik, Stephan, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C. Meyer, et al. 2017. “A Global Staphylococcus Aureus Proteome Resource Applied to the in Vivo Characterization of Host-Pathogen Interactions.” Scientific Reports 7 (1): 9718. https://doi.org/10.1038/s41598-017-10059-w. Cite
Price, Nathan D., Andrew T. Magis, John C. Earls, Gustavo Glusman, Roie Levy, Christopher Lausted, Daniel T. McDonald, et al. 2017. “A Wellness Study of 108 Individuals Using Personal, Dense, Dynamic Data Clouds.” Nature Biotechnology. https://doi.org/10.1038/nbt.3870. Cite
Atapattu, Lakmali, Nayanendu Saha, Chanly Chheang, Moritz F. Eissman, Kai Xu, Mary E. Vail, Linda Hii, et al. 2016. “An Activated Form of ADAM10 Is Tumor Selective and Regulates Cancer Stem-like Cells and Tumor Growth.” The Journal of Experimental Medicine 213 (9): 1741–57. https://doi.org/10.1084/jem.20151095. Cite
Hoofnagle, A. N., J. R. Whiteaker, S. A. Carr, E. Kuhn, T. Liu, S. A. Massoni, S. N. Thomas, et al. 2016. “Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays.” Clinical Chemistry 62 (January):48–69. https://doi.org/10.1373/clinchem.2015.250563. Cite
Maixner, F., B. Krause-Kyora, D. Turaev, A. Herbig, M. R. Hoopmann, J. L. Hallows, U. Kusebauch, et al. 2016. “The 5300-Year-Old Helicobacter Pylori Genome of the Iceman.” Science 351:162–65. https://doi.org/10.1126/science.aad2545. Cite
Deutsch, Eric W., Christopher M. Overall, Jennifer E. Van Eyk, Mark S. Baker, Young-Ki Paik, Susan T. Weintraub, Lydie Lane, et al. 2016. “Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.6b00392. Cite
Qin, Shizhen, Yong Zhou, Li Gray, Ulrike Kusebauch, Laurence McEvoy, Daniel J. Antoine, Lucy Hampson, et al. 2016. “Identification of Organ-Enriched Protein Biomarkers of Acute Liver Injury by Targeted Quantitative Proteomics of Blood in Acetaminophen- and Carbon-Tetrachloride-Treated Mouse Models and Acetaminophen Overdose Patients.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.6b00547. Cite
Craciun, Florin L., Vanesa Bijol, Amrendra K. Ajay, Poornima Rao, Ramya K. Kumar, John Hutchinson, Oliver Hofmann, et al. 2016. “RNA Sequencing Identifies Novel Translational Biomarkers of Kidney Fibrosis.” Journal of the American Society of Nephrology: JASN 27 (6): 1702–13. https://doi.org/10.1681/ASN.2015020225. Cite
Kusebauch, Ulrike, David S. Campbell, Eric W. Deutsch, Caroline S. Chu, Douglas A. Spicer, Mi-Youn Brusniak, Joseph Slagel, et al. 2016. “Human SRMAtlas: A Resource of Targeted Assays to Quantify the Complete Human Proteome.” Cell 166 (3): 766–78. https://doi.org/10.1016/j.cell.2016.06.041. Cite
Keller, A., S. L. Bader, U. Kusebauch, D. Shteynberg, L. Hood, and R. L. Moritz. 2015. “Opening a SWATH Window on Post-Translational Modifications: Automated Pursuit of Modified Peptides.” Molecular & Cellular Proteomics : MCP, December. https://doi.org/10.1074/mcp.M115.054478. Cite
Swearingen, K. E., J. M. Winget, M. R. Hoopmann, U. Kusebauch, and R. L. Moritz. 2015. “Decreased Gap Width in a Cylindrical High-Field Asymmetric Waveform Ion Mobility Spectrometry Device Improves Protein Discovery.” Analytical Chemistry 87 (December):12230–37. https://doi.org/10.1021/acs.analchem.5b03199. Cite
Craciun, F. L., V. Bijol, A. K. Ajay, P. Rao, R. K. Kumar, J. Hutchinson, O. Hofmann, et al. 2015. “RNA Sequencing Identifies Novel Translational Biomarkers of Kidney Fibrosis.” Journal of the American Society of Nephrology : JASN, October. https://doi.org/10.1681/ASN.2015020225. Cite
Deutsch, E. W., Z. Sun, D. Campbell, U. Kusebauch, C. S. Chu, L. Mendoza, D. Shteynberg, G. S. Omenn, and R. L. Moritz. 2015. “State of the Human Proteome in 2014/2015 As Viewed through PeptideAtlas: Enhancing Accuracy and Coverage through the AtlasProphet.” Journal of Proteome Research 14 (September):3461–73. https://doi.org/10.1021/acs.jproteome.5b00500. Cite
Sangar, Vineet, Cory C. Funk, Ulrike Kusebauch, D. Campbell, Robert L. Moritz, and Nathan D. Price. 2014. “Quantitative Proteomic Analysis Reveals Effects of Epidermal Growth Factor Receptor (EGFR) on Invasion-Promoting Proteins Secreted by Glioblastoma Cells.” Molecular & Cellular Proteomics: MCP 13 (10): 2618–31. https://doi.org/10.1074/mcp.M114.040428. Cite
Kusebauch, U., C. Ortega, A. Ollodart, R. S. Rogers, D. R. Sherman, R. L. Moritz, and C. Grundner. 2014. “Mycobacterium Tuberculosis Supports Protein Tyrosine Phosphorylation.” Proceedings of the National Academy of Sciences of the United States of America, June. Cite
Surmann, Kristin, Stephan Michalik, Petra Hildebrandt, Philipp Gierok, Maren Depke, Lars Brinkmann, Jörg Bernhardt, et al. 2014. “Comparative Proteome Analysis Reveals Conserved and Specific Adaptation Patterns of Staphylococcus Aureus after Internalization by Different Types of Human Non-Professional Phagocytic Host Cells.” Front Microbiol 5:392. https://doi.org/10.3389/fmicb.2014.00392. Cite
Kusebauch, U., E. W. Deutsch, D. S. Campbell, Z. Sun, T. Farrah, and R. L. Moritz. 2014. “Using PeptideAtlas, SRMAtlas, and PASSEL: Comprehensive Resources for Discovery and Targeted Proteomics.” Current Protocols in Bioinformatics / Editoral Board, Andreas D. Baxevanis … [et Al.] 46:13 25 1-13 25 28. Cite
Mercier, Sarah K., Heather Donaghy, Rachel A. Botting, Stuart G. Turville, Andrew N. Harman, Najla Nasr, Hong Ji, et al. 2013. “The Microvesicle Component of HIV-1 Inocula Modulates Dendritic Cell Infection and Maturation and Enhances Adhesion to and Activation of T Lymphocytes.” PLoS Pathogens 9 (10): e1003700. https://doi.org/10.1371/journal.ppat.1003700. Cite
Tauro, B. J., R. A. Mathias, D. W. Greening, S. K. Gopal, H. Ji, E. A. Kapp, B. M. Coleman, et al. 2013. “Oncogenic H-Ras Reprograms Madin-Darby Canine Kidney (MDCK) Cell-Derived Exosomal Proteins Following Epithelial-Mesenchymal Transition.” Mol Cell Proteomics, May. Cite
Huttenhain, R., S. Surinova, R. Ossola, Z. Sun, D. Campbell, F. Cerciello, R. Schiess, et al. 2013. “N-Glycoprotein SRMAtlas: A Resource of Mass-Spectrometric Assays for N-Glycosites Enabling Consistent and Multiplexed Protein Quantification for Clinical Applications.” Molecular & Cellular Proteomics : MCP, February. Cite
Picotti, P., M. Clement-Ziza, H. Lam, D. S. Campbell, A. Schmidt, E. W. Deutsch, H. Rost, et al. 2013. “A Complete Mass-Spectrometric Map of the Yeast Proteome Applied to Quantitative Trait Analysis.” Nature, January. Cite
Huttenhain, R., M. Soste, N. Selevsek, H. Rost, A. Sethi, C. Carapito, T. Farrah, et al. 2012. “Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics.” Science Translational Medicine 4 (142): 142ra94. Cite
Brusniak, M. Y., C. S. Chu, U. Kusebauch, M. J. Sartain, J. D. Watts, and R. L. Moritz. 2012. “An Assessment of Current Bioinformatic Solutions for Analyzing LC-MS Data Acquired by Selected Reaction Monitoring Technology.” Proteomics 12 (8): 1176–84. Cite
Bislev, S. L., U. Kusebauch, M. C. Codrea, R. J. Beynon, V. M. Harman, C. M. Rontved, R. Aebersold, R. L. Moritz, and E. Bendixen. 2012. “Quantotypic Properties of QconCAT Peptides Targeting Bovine Host Response to Streptococcus Uberis.” Journal of Proteome Research 11 (3): 1832–43. Cite
Farrah, T., E. W. Deutsch, R. Kreisberg, Z. Sun, D. S. Campbell, L. Mendoza, U. Kusebauch, et al. 2012. “PASSEL: The PeptideAtlas SRM Experiment Library.” Proteomics, February. Cite
Brusniak, M. Y., S. T. Kwok, M. Christiansen, D. Campbell, L. Reiter, P. Picotti, U. Kusebauch, et al. 2011. “ATAQS: A Computational Software Tool for High Throughput Transition Optimization and Validation for Selected Reaction Monitoring Mass Spectrometry.” BMC Bioinformatics 12 (1): 78. Cite
Ramos, H., P. Shannon, M. Y. Brusniak, U. Kusebauch, R. L. Moritz, and R. Aebersold. 2011. “The Protein Information and Property Explorer 2: Gaggle-like Exploration of Biological Proteomic Data within One Webpage.” Proteomics 11 (1): 154–58. Cite