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Robert Moritz

Robert Moritz, PhD

Professor

ISB

Dr. Robert Moritz, a native of Australia, joined the ISB faculty in mid 2008 as Associate Professor and Director of Proteomics. Dr. Moritz began his work in 1983 in the Joint Protein Structure laboratory of Prof. Richard J. Simpson (JPSL-Ludwig Institute for Cancer Research, and The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia). During his 25 years at JPSL, Dr. Moritz designed and implemented a number of technologies currently used in many proteomics laboratories across the globe. Examples include technologies such as the development of micro-chromatography for proteomics from the late 1980’s to its current day implementation, a micro-fractionation technique widely used by many laboratories worldwide. His collaborative research into cytokine biochemistry, protein-receptor chemistry and cellular biochemistry culminated in the novel identification of a number of proteins (e.g., IL-6, IL-9 A33 ligand, DIABLO, as well as several others), their interacting partners, and 3-dimensional structures of their cell surface receptors important in human health concerns such as cancer and inflammation. During his time at JPSL, Dr. Moritz progressed through the ranks whilst obtaining his Bachelor’s degree in Biochemistry with first-class Honors, and his Ph.D., from the University of Melbourne.

Dr. Moritz has brought wide-ranging skills and expertise to ISB, much of it drawn from his Australian experience. There, in 2005, he conceptualized a shared proteomics high-performance computing system, organized a consortia of proteomic scientists from all states in Australia, and proposed a computational system specifically for proteomics data analysis for all Australian researchers to access. For this work, in 2006, he was awarded an enabling grant from the Australian National Health and Medical Research Council worth AUS$2M. With that award, he established a bioinformatics center in Australia that enabled proteomic researchers anywhere in the country to analyze mass spectrometry data. It was the first effort on a national scale to bring proteomic data analysis and algorithms to any researcher in the whole country without the need for them to build their own bioinformatics group. In late 2006, the Australian Proteomics Computational Facility (APCF, www.apcf.edu.au) was inaugurated, and Dr. Moritz remains as Director of the APCF. The dedicated proteomics data analysis facility is equipped with a 1000 CPU high-performance computing cluster, and full-time software engineers for the continued development of proteomics algorithms and data validation. This facility serves all researchers in Australia and others regardless of their global geographical location. He is continuing that work at ISB by expanding the ISB proteomics centre into a national facility with online tools for data analysis.

PhD, University of Melbourne, Australia

Proteomics, protein chemistry, technology development

Zelter, Alex, Michael Riffle, David D. Shteynberg, Guo Zhong, Ellen B. Riddle, Michael R. Hoopmann, Daniel Jaschob, et al. 2024. “Detection and Quantification of Drug–Protein Adducts in Human Liver.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.4c00663. Cite
Omenn, Gilbert S., Lydie Lane, Christopher M. Overall, Cecilia Lindskog, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, et al. 2024. “The 2023 Report on the Proteome from the HUPO Human Proteome Project.” Journal of Proteome Research 23 (2): 532–49. https://doi.org/10.1021/acs.jproteome.3c00591. Cite
Rios, Kelly T., James P. McGee, Aswathy Sebastian, Robert L. Moritz, Marina Feric, Sabrina Absalon, Kristian E. Swearingen, and Scott E. Lindner. 2024. “Global Release of Translational Repression Across Plasmodium’s Host-to-Vector Transmission Event.” BioRxiv: The Preprint Server for Biology, 2024.02.01.577866. https://doi.org/10.1101/2024.02.01.577866. Cite Download
Nagar, Rupa, Stefano S. Garcia Castillo, Maria Pinzon-Ortiz, Sharon Patray, Alida Coppi, Sachie Kanatani, Robert L. Moritz, Kristian E. Swearingen, Michael A. J. Ferguson, and Photini Sinnis. 2024. “The Major Surface Protein of Malaria Sporozoites Is GPI-Anchored to the Plasma Membrane.” The Journal of Biological Chemistry 300 (8): 107557. https://doi.org/10.1016/j.jbc.2024.107557. Cite
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
Pflieger, Lance, Kengo Watanabe, Max Robinson, Gustavo Glusman, Jodi Lapidus, Oliver Fiehn, Robert Moritz, and Noa Rappaport. 2023. “PROSPECTIVE MULTI-OMIC ANALYSIS OF HUMAN LONGEVITY COHORTS IDENTIFIES ANALYTE NETWORKS ASSOCIATED WITH LONGEVITY.” Innovation in Aging 7 (Suppl 1): 691–92. https://doi.org/10.1093/geroni/igad104.2245. Cite Download
Jiang, Yuming, Devasahayam Arokia Balaya Rex, Dina Schuster, Benjamin A. Neely, Germán L. Rosano, Norbert Volkmar, Amanda Momenzadeh, et al. 2023. “Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry.” ArXiv, arXiv:2311.07791v1. Cite
Mandal, Kamal, Gianina Wicaksono, Clinton Yu, Jarrett J. Adams, Michael R. Hoopmann, William C. Temple, Adila Izgutdina, et al. 2023. “Structural Surfaceomics Reveals an AML-Specific Conformation of Integrin Β2 as a CAR T Cellular Therapy Target.” Nature Cancer 4 (11): 1592–1609. https://doi.org/10.1038/s43018-023-00652-6. 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
Prensner, John R., Jennifer G. Abelin, Leron W. Kok, Karl R. Clauser, Jonathan M. Mudge, Jorge Ruiz-Orera, Michal Bassani-Sternberg, Robert L. Moritz, Eric W. Deutsch, and Sebastiaan van Heesch. 2023. “What Can Ribo-Seq, Immunopeptidomics, and Proteomics Tell Us About the Noncanonical Proteome?” Molecular & Cellular Proteomics: MCP 22 (9): 100631. https://doi.org/10.1016/j.mcpro.2023.100631. Cite Download
Midha, Mukul K., Charu Kapil, Michal Maes, David H. Baxter, Seamus R. Morrone, Timothy J. Prokop, and Robert L. Moritz. 2023. “Vacuum Insulated Probe Heated Electrospray Ionization Source Enhances Microflow Rate Chromatography Signals in the Bruker TimsTOF Mass Spectrometer.” Journal of Proteome Research 22 (7): 2525–37. https://doi.org/10.1021/acs.jproteome.3c00305. 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
Jennison, Charlie, Janna M. Armstrong, Dorender A. Dankwa, Nina Hertoghs, Sudhir Kumar, Biley A. Abatiyow, Myo Naung, et al. 2023. “Plasmodium GPI-Anchored Micronemal Antigen Is Essential for Parasite Transmission through the Mosquito Host.” Molecular Microbiology. https://doi.org/10.1111/mmi.15078. Cite Download
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
Sandmann, Clara-L., Jana F. Schulz, Jorge Ruiz-Orera, Marieluise Kirchner, Matthias Ziehm, Eleonora Adami, Maike Marczenke, et al. 2023. “Evolutionary Origins and Interactomes of Human, Young Microproteins and Small Peptides Translated from Short Open Reading Frames.” Molecular Cell 83 (6): 994-1011.e18. https://doi.org/10.1016/j.molcel.2023.01.023. 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
Zhang, Yu-Hang, Michael H. Cho, Jarrett D. Morrow, Peter J. Castaldi, Craig P. Hersh, Mukul K. Midha, Michael R. Hoopmann, Sharon M. Lutz, Robert L. Moritz, and Edwin K. Silverman. 2023. “Integrating Genetics, Transcriptomics, and Proteomics in Lung Tissue to Investigate COPD.” American Journal of Respiratory Cell and Molecular Biology. https://doi.org/10.1165/rcmb.2022-0302OC. Cite
Deutsch, Eric W., Luis Mendoza, David D. Shteynberg, Michael R. Hoopmann, Zhi Sun, Jimmy K. Eng, and Robert L. Moritz. 2023. “Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.” Journal of Proteome Research 22 (2): 615–24. https://doi.org/10.1021/acs.jproteome.2c00624. Cite
Hoopmann, Michael R., David D. Shteynberg, Alex Zelter, Michael Riffle, Andrew S. Lyon, David A. Agard, Qing Luan, et al. 2023. “Improved Analysis of Cross-Linking Mass Spectrometry Data with Kojak 2.0, Advanced by Integration into the Trans-Proteomic Pipeline.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00670. Cite
Kertesz-Farkas, Attila, Frank Lawrence Nii Adoquaye Acquaye, Kishankumar Bhimani, Jimmy K. Eng, William E. Fondrie, Charles Grant, Michael R. Hoopmann, et al. 2023. “The Crux Toolkit for Analysis of Bottom-Up Tandem Mass Spectrometry Proteomics Data.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00615. Cite Download
Riffle, Michael, Michael R. Hoopmann, Daniel Jaschob, Guo Zhong, Robert L. Moritz, Michael J. MacCoss, Trisha N. Davis, Nina Isoherranen, and Alex Zelter. 2022. “Discovery and Visualization of Uncharacterized Drug–Protein Adducts Using Mass Spectrometry.” Analytical Chemistry 94 (8): 3501–9. https://doi.org/10.1021/acs.analchem.1c04101. Cite Download
Omenn, Gilbert S., Lydie Lane, Christopher M. Overall, Charles Pineau, Nicolle H. Packer, Ileana M. Cristea, Cecilia Lindskog, et al. 2022. “The 2022 Report on the Human Proteome from the HUPO Human Proteome Project.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.2c00498. Cite
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
Mandal, Kamal, Gianina Wicaksono, Clinton Yu, Jarrett J Adams, Michael R Hoopmann, William C Temple, Bonell Patino Escobar, et al. 2022. “Structural Surfaceomics Reveals an AML-Specific Conformation of Integrin-Β2 As an Immunotherapeutic Target.” Blood 140 (Supplement 1): 867–68. https://doi.org/10.1182/blood-2022-162697. Cite
Deutsch, Eric, Luis Mendoza, David Shteynberg, Michael Hoopmann, Zhi Sun, Jimmy Eng, and Robert Moritz. 2022. “The Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite.” ChemRxiv. https://doi.org/10.26434/chemrxiv-2022-3c75n. Cite Download
Jennison, Charlie, Janna M. Gibson, Nina Hertoghs, Dorender A. Dankwa, Sudhir Kumar, Biley A. Abatiyow, Myo Naung, et al. 2022. “Plasmodium GPI-Anchored Micronemal Antigen Is Essential for Parasite Transmission through the Mosquito Host.” bioRxiv. https://doi.org/10.1101/2022.02.24.481744. Cite Download
Zhang, Y.-H., J. Morrow, P. Castaldi, S. Lutz, C.P. Hersh, M.H. Cho, M. Hoopmann, M. Midha, R. Moritz, and E.K. Silverman. 2022. “Integrating Proteomics, Transcriptomics and Genetics in COPD Lung Tissue Samples.” In C66. COPD: GENETICS, GENOMICS, AND EPIGENETICS, A4662–A4662. American Thoracic Society. https://doi.org/10.1164/ajrccm-conference.2022.205.1_MeetingAbstracts.A4662. 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
Mudge, Jonathan M., Jorge Ruiz-Orera, John R. Prensner, Marie A. Brunet, Ferriol Calvet, Irwin Jungreis, Jose Manuel Gonzalez, et al. 2022. “Standardized Annotation of Translated Open Reading Frames.” Nature Biotechnology 40 (7): 994–99. https://doi.org/10.1038/s41587-022-01369-0. 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
Nissa, Mehar Un, Panga Jaipal Reddy, Nevil Pinto, Zhi Sun, Biplab Ghosh, Robert L. Moritz, Mukunda Goswami, and Sanjeeva Srivastava. 2022. “The PeptideAtlas of a Widely Cultivated Fish Labeo Rohita: A Resource for the Aquaculture Community.” Scientific Data 9 (1): 171. https://doi.org/10.1038/s41597-022-01259-9. Cite Download
Lindner, Scott E., Kristian E. Swearingen, Melanie J. Shears, Aswathy Sebastian, Michael P. Walker, Erin N. Vrana, Kevin J. Hart, et al. 2022. “Addendum: Transcriptomics and Proteomics Reveal Two Waves of Translational Repression during the Maturation of Malaria Parasite Sporozoites.” Nature Communications 13 (1): 283. https://doi.org/10.1038/s41467-021-27767-7. Cite Download
Sun, Bingyun, Cynthia Lorang, Shizhen Qin, Yijuan Zhang, Ken Liu, Gray Li, Zhi Sun, et al. 2021. “Mouse Organ-Specific Proteins and Functions.” Cells 10 (12): 3449. https://doi.org/10.3390/cells10123449. Cite Download
Nissa, Mehar Un, Nevil Pinto, Arijit Mukherjee, Panga Jaipal Reddy, Biplab Ghosh, Zhi Sun, Saicharan Ghantasala, et al. 2021. “Organ-Based Proteome and Post-Translational Modification Profiling of a Widely Cultivated Tropical Water Fish, Labeo Rohita.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.1c00759. 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
Zhang, Yu-Hang, Michael R. Hoopmann, Peter J. Castaldi, Kirsten A. Simonsen, Mukul K. Midha, Michael H. Cho, Gerard J. Criner, et al. 2021. “Lung Proteomic Biomarkers Associated with Chronic Obstructive Pulmonary Disease.” American Journal of Physiology. Lung Cellular and Molecular Physiology 321 (6): L1119–30. https://doi.org/10.1152/ajplung.00198.2021. Cite
Omenn, Gilbert S., Lydie Lane, Christopher M. Overall, Young-Ki Paik, Ileana M. Cristea, Fernando J. Corrales, Cecilia Lindskog, et al. 2021. “Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project.” Journal of Proteome Research 20 (12): 5227–40. https://doi.org/10.1021/acs.jproteome.1c00590. Cite
Deutsch, Eric W., Gilbert S. Omenn, Zhi Sun, Michal Maes, Maria Pernemalm, Krishnan K. Palaniappan, Natasha Letunica, et al. 2021. “Advances and Utility of the Human Plasma Proteome.” Journal of Proteome Research 20 (12): 5241–63. https://doi.org/10.1021/acs.jproteome.1c00657. Cite
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
Steel, Ryan W. J., Vladimir Vigdorovich, Nicholas Dambrauskas, Brandon K. Wilder, Silvia A. Arredondo, Debashree Goswami, Sudhir Kumar, et al. 2021. “Platelet Derived Growth Factor Receptor β (PDGFRβ) Is a Host Receptor for the Human Malaria Parasite Adhesin TRAP.” Scientific Reports 11 (1): 11328. https://doi.org/10.1038/s41598-021-90722-5. Cite Download
Bobe, Jason R., Brandon L. Jutras, Elizabeth J. Horn, Monica E. Embers, Allison Bailey, Robert L. Moritz, Ying Zhang, et al. 2021. “Recent Progress in Lyme Disease and Remaining Challenges.” Frontiers in Medicine 8:666554. https://doi.org/10.3389/fmed.2021.666554. Cite Download
Reales-Calderón, J. A., Z. Sun, V. Mascaraque, E. Pérez-Navarro, V. Vialás, E. W. Deutsch, R. L. Moritz, C. Gil, J. L. Martínez, and G. Molero. 2021. “A Wide-Ranging Pseudomonas Aeruginosa PeptideAtlas Build: A Useful Proteomic Resource for a Versatile Pathogen.” Journal of Proteomics 239:104192. https://doi.org/10.1016/j.jprot.2021.104192. Cite Download
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
Cobb, David W., Heather M. Kudyba, Alejandra Villegas, Michael R. Hoopmann, Rodrigo P. Baptista, Baylee Bruton, Michelle Krakowiak, Robert L. Moritz, and Vasant Muralidharan. 2021. “A Redox-Active Crosslinker Reveals an Essential and Inhibitable Oxidative Folding Network in the Endoplasmic Reticulum of Malaria Parasites.” PLoS Pathogens 17 (2): e1009293. https://doi.org/10.1371/journal.ppat.1009293. Cite Download
Kailash, Vidur, Luis Mendoza, Robert L. Moritz, and Michael R. Hoopmann. 2021. “SPACEPro: A Software Tool for Analysis of Protein Sample Cleavage for Tandem Mass Spectrometry.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.0c00928. Cite
Weerakoon, Harshi, Jeremy Potriquet, Alok K. Shah, Sarah Reed, Buddhika Jayakody, Charu Kapil, Mukul K. Midha, et al. 2020. “A Primary Human T-Cell Spectral Library to Facilitate Large Scale Quantitative T-Cell Proteomics.” Scientific Data 7 (1): 412. https://doi.org/10.1038/s41597-020-00744-3. Cite Download
Omenn, Gilbert S., Lydie Lane, Christopher M. Overall, Ileana M. Cristea, Fernando J. Corrales, Cecilia Lindskog, Young-Ki Paik, et al. 2020. “Research on the Human Proteome Reaches a Major Milestone: >90% of Predicted Human Proteins Now Credibly Detected, According to the HUPO Human Proteome Project.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.0c00485. Cite
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
Leitner, Alexander, Alexandre M. J. J. Bonvin, Christoph H. Borchers, Robert J. Chalkley, Julia Chamot-Rooke, Colin W. Combe, Jürgen Cox, et al. 2020. “Toward Increased Reliability, Transparency, and Accessibility in Cross-Linking Mass Spectrometry.” Structure (London, England: 1993) 28 (11): 1259–68. https://doi.org/10.1016/j.str.2020.09.011. Cite Download
Martínez Arbas, Susana, Shaman Narayanasamy, Malte Herold, Laura A. Lebrun, Michael R. Hoopmann, Sujun Li, Tony J. Lam, et al. 2020. “Roles of Bacteriophages, Plasmids and CRISPR Immunity in Microbial Community Dynamics Revealed Using Time-Series Integrated Meta-Omics.” Nature Microbiology. https://doi.org/10.1038/s41564-020-00794-8. Cite Download