Ulrike Kusebauch, PhD

Senior Research Scientist

Moritz Lab

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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

2323737 2RQKSFR5 kusebauch 1 chicago-author-date-16th-edition 50 date desc year 1 1 8058 https://isbscience.org/wp-content/plugins/zotpress/

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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. http://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. http://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. http://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. http://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). http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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. http://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