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Eric Deutsch

Eric Deutsch, PhD

Principal Scientist

Moritz Lab

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  • Biography
  • Research Interests
  • Publications

Dr. Deutsch’s research activities include software development for the analysis and integration of data for systems biology research. He is the lead designer for the Systems Biology Experiment Analysis Management System (SBEAMS). He contributes the development of minimum information standards, data formats, and databases for proteomics as chair of the HUPO Proteomics Standards Initiative (PSI). Dr. Deutsch  leads of the Trans-Proteomic Pipeline project, which is a free and open-source suite of tools for the processing and analysis of proteomics tandem mass spectrometry data. He also heads the PeptideAtlas Project, which aims to collect proteomics mass spectrometry data from labs around the world to synthesize a master list of observed peptides and proteins and disseminate the results back to the community.

Dr. Deutsch’s research activities include software development for the analysis and integration of data for systems biology research. He is the lead designer for the Systems Biology Experiment Analysis Management System (SBEAMS). He contributes the development of minimum information standards, data formats, and databases for proteomics as chair of the HUPO Proteomics Standards Initiative (PSI). Dr. Deutsch is the leader of the Trans-Proteomic Pipeline project, which aims to provide a free and open-source suite of tools for the processing and analysis of proteomics tandem mass spectrometry data. He also heads the PeptideAtlas Project, which aims to collect proteomics mass spectrometry data from labs around the world to synthesize a master list of observed peptides and proteins and disseminate the results back to the community.
Deutsch, Eric W., Leron W. Kok, Jonathan M. Mudge, Jorge Ruiz-Orera, Ivo Fierro-Monti, Zhi Sun, Jennifer G. Abelin, et al. 2024. “High-Quality Peptide Evidence for Annotating Non-Canonical Open Reading Frames as Human Proteins.” BioRxiv: The Preprint Server for Biology, 2024.09.09.612016. https://doi.org/10.1101/2024.09.09.612016. Cite
Camacho, Oscar J. M., Kerry A. Ramsbottom, Ananth Prakash, Zhi Sun, Yasset Perez Riverol, Emily Bowler-Barnett, Maria Martin, et al. 2024. “Phosphorylation in the Plasmodium Falciparum Proteome: A Meta-Analysis of Publicly Available Data Sets.” Journal of Proteome Research 23 (12): 5326–41. https://doi.org/10.1021/acs.jproteome.4c00418. Cite
Geyer, Philipp E., Daniel Hornburg, Maria Pernemalm, Stefanie M. Hauck, Krishnan K. Palaniappan, Vincent Albrecht, Laura F. Dagley, et al. 2024. “The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends.” Journal of Proteome Research 23 (12): 5279–95. https://doi.org/10.1021/acs.jproteome.4c00586. Cite
Klein, Joshua, Henry Lam, Tytus D. Mak, Wout Bittremieux, Yasset Perez-Riverol, Ralf Gabriels, Jim Shofstahl, et al. 2024. “The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: MzSpecLib and MzPAF.” Analytical Chemistry 96 (46): 18491–501. https://doi.org/10.1021/acs.analchem.4c04091. Cite
Omenn, Gilbert S., Sandra Orchard, Lydie Lane, Cecilia Lindskog, Charles Pineau, Christopher M. Overall, Bogdan Budnik, et al. 2024. “The 2024 Report on the Human Proteome from the HUPO Human Proteome Project.” Journal of Proteome Research 23 (12): 5296–5311. https://doi.org/10.1021/acs.jproteome.4c00776. Cite
Zhang, Nathan H., and Eric W. Deutsch. 2024. “SpectiCal: M/z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions.” Journal of Proteome Research 23 (4): 1519–30. https://doi.org/10.1021/acs.jproteome.3c00882. 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
Wijk, Klaas J. van, Tami Leppert, Zhi Sun, Isabell Guzchenko, Erica Debley, Georgia Sauermann, Pratyush Routray, Luis Mendoza, Qi Sun, and Eric W. Deutsch. 2024. “The Zea Mays PeptideAtlas: A New Maize Community Resource.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.4c00320. Cite
Ramsbottom, Kerry A., Ananth Prakash, Yasset Perez-Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J. Kundu, Emily Bowler-Barnett, et al. 2024. “Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome.” Journal of Proteome Research 23 (7): 2518–31. https://doi.org/10.1021/acs.jproteome.4c00187. Cite Download
Jones, Andrew R., Eric W. Deutsch, and Juan Antonio Vizcaíno. 2023. “Is DIA Proteomics Data FAIR? Current Data Sharing Practices, Available Bioinformatics Infrastructure and Recommendations for the Future.” PROTEOMICS 23 (7–8): 2200014. https://doi.org/10.1002/pmic.202200014. Cite Download
Wijk, Klaas J. van, Tami Leppert, Zhi Sun, Alyssa Kearly, Margaret Li, Luis Mendoza, Isabell Guzchenko, et al. 2023. “Detection of the Arabidopsis Proteome and Its Post-Translational Modifications and the Nature of the Unobserved (Dark) Proteome in PeptideAtlas.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.3c00536. Cite
Ramsbottom, Kerry A., Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Zhi Sun, Deepti J. Kundu, Emily Bowler-Barnett, et al. 2023. “A Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signalling across the Rice Pan-Genome.” BioRxiv: The Preprint Server for Biology, 2023.11.17.567512. https://doi.org/10.1101/2023.11.17.567512. Cite Download
Wijk, Klaas J. van, Stephane Bentolila, Tami Leppert, Qi Sun, Zhi Sun, Luis Mendoza, Margaret Li, and Eric W. Deutsch. 2023. “Detection and Editing of the Updated Arabidopsis Plastid- and Mitochondrial-Encoded Proteomes through PeptideAtlas.” Plant Physiology, kiad572. https://doi.org/10.1093/plphys/kiad572. Cite
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
Wijk, Klaas J. van, Tami Leppert, Zhi Sun, and Eric W. Deutsch. 2023. “Does the Ubiquitination Degradation Pathway Really Reach inside of the Chloroplast? A Re-Evaluation of Mass Spectrometry-Based Assignments of Ubiquitination.” Journal of Proteome Research 22 (6): 2079–91. https://doi.org/10.1021/acs.jproteome.3c00178. Cite
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
Glen, Amy K., Chunyu Ma, Luis Mendoza, Finn Womack, E. C. Wood, Meghamala Sinha, Liliana Acevedo, et al. 2023. “ARAX: A Graph-Based Modular Reasoning Tool for Translational Biomedicine.” Bioinformatics (Oxford, England) 39 (3): btad082. https://doi.org/10.1093/bioinformatics/btad082. Cite Download
Neely, Benjamin A., Viktoria Dorfer, Lennart Martens, Isabell Bludau, Robbin Bouwmeester, Sven Degroeve, Eric W. Deutsch, et al. 2023. “Toward an Integrated Machine Learning Model of a Proteomics Experiment.” Journal of Proteome Research 22 (3): 681–96. https://doi.org/10.1021/acs.jproteome.2c00711. Cite Download
Rehfeldt, Tobias G., Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin A. Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaíno, and Eric W. Deutsch. 2023. “ProteomicsML: An Online Platform for Community-Curated Data Sets and Tutorials for Machine Learning in Proteomics.” Journal of Proteome Research 22 (2): 632–36. https://doi.org/10.1021/acs.jproteome.2c00629. Cite Download
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
Deutsch, Eric W., Juan Antonio Vizcaíno, Andrew R. Jones, Pierre-Alain Binz, Henry Lam, Joshua Klein, Wout Bittremieux, et al. 2023. “Proteomics Standards Initiative at Twenty Years: Current Activities and Future Work.” Journal of Proteome Research 22 (2): 287–301. https://doi.org/10.1021/acs.jproteome.2c00637. Cite Download
Deutsch, Eric W., Nuno Bandeira, Yasset Perez-Riverol, Vagisha Sharma, Jeremy J. Carver, Luis Mendoza, Deepti J. Kundu, et al. 2022. “The ProteomeXchange Consortium at 10 Years: 2023 Update.” Nucleic Acids Research, gkac1040. https://doi.org/10.1093/nar/gkac1040. Cite Download 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
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
Glen, Amy K., Chunyu Ma, Luis Mendoza, Finn Womack, E. C. Wood, Meghamala Sinha, Liliana Acevedo, et al. 2022. “ARAX: A Graph-Based Modular Reasoning Tool for Translational Biomedicine.” bioRxiv. https://doi.org/10.1101/2022.08.12.503810. Cite Download
Rehfeldt, Tobias, Ralf Gabriels, Robbin Bouwmeester, Siegfried Gessulat, Benjamin Neely, Magnus Palmblad, Yasset Perez-Riverol, Tobias Schmidt, Juan Antonio Vizcaíno, and Eric Deutsch. 2022. “ProteomicsML: An Online Platform for Community-Curated Datasets and Tutorials for Machine Learning in Proteomics.” ChemRxiv. https://doi.org/10.26434/chemrxiv-2022-2s6kx. Cite Download
Jones, Andrew, Eric Deutsch, and Juan Antonio Vizcaino. 2022. “Is DIA Proteomics Data FAIR? Current Data Sharing Practices, Available Bioinformatics Infrastructure and Recommendations for the Future – Jones – PROTEOMICS – Wiley Online Library.” 2022. https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200014. Cite
Wood, E. C., Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, et al. 2022. “RTX-KG2: A System for Building a Semantically Standardized Knowledge Graph for Translational Biomedicine.” BMC Bioinformatics 23 (1): 400. https://doi.org/10.1186/s12859-022-04932-3. 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
Ramsbottom, Kerry A., Ananth Prakash, Yasset Perez Riverol, Oscar Martin Camacho, Maria-Jesus Martin, Juan Antonio Vizcaíno, Eric W. Deutsch, and Andrew R. Jones. 2022. “Method for Independent Estimation of the False Localization Rate for Phosphoproteomics.” Journal of Proteome Research 21 (7): 1603–15. https://doi.org/10.1021/acs.jproteome.1c00827. Cite
Luo, Xiyang, Wout Bittremieux, Johannes Griss, Eric W. Deutsch, Timo Sachsenberg, Lev I. Levitsky, Mark V. Ivanov, et al. 2022. “A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics.” Journal of Proteome Research 21 (6): 1566–74. https://doi.org/10.1021/acs.jproteome.2c00069. Cite Download
Kalyuzhnyy, Anton, Patrick A. Eyers, Claire E. Eyers, Emily Bowler-Barnett, Maria J. Martin, Zhi Sun, Eric W. Deutsch, and Andrew R. Jones. 2022. “Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation.” Journal of Proteome Research 21 (6): 1510–24. https://doi.org/10.1021/acs.jproteome.2c00131. Cite Download
LeDuc, Richard D., Eric W. Deutsch, Pierre-Alain Binz, Ryan T. Fellers, Anthony J. Cesnik, Joshua A. Klein, Tim Van Den Bossche, et al. 2022. “Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms.” Journal of Proteome Research 21 (4): 1189–95. https://doi.org/10.1021/acs.jproteome.1c00771. 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
Wijk, Klaas J. van, Tami Leppert, Qi Sun, Sascha S. Boguraev, Zhi Sun, Luis Mendoza, and Eric W. Deutsch. 2021. “The Arabidopsis PeptideAtlas: Harnessing Worldwide Proteomics Data to Create a Comprehensive Community Proteomics Resource.” The Plant Cell, koab211. https://doi.org/10.1093/plcell/koab211. Cite
Dai, Chengxin, Anja Füllgrabe, Julianus Pfeuffer, Elizaveta M. Solovyeva, Jingwen Deng, Pablo Moreno, Selvakumar Kamatchinathan, et al. 2021. “A Proteomics Sample Metadata Representation for Multiomics Integration and Big Data Analysis.” Nature Communications 12 (1): 5854. https://doi.org/10.1038/s41467-021-26111-3. Cite
Deutsch, Eric W., Yasset Perez-Riverol, Jeremy Carver, Shin Kawano, Luis Mendoza, Tim Van Den Bossche, Ralf Gabriels, et al. 2021. “Universal Spectrum Identifier for Mass Spectra.” Nature Methods 18 (7): 768–70. https://doi.org/10.1038/s41592-021-01184-6. Cite Download
Bandeira, Nuno, Eric W. Deutsch, Oliver Kohlbacher, Lennart Martens, and Juan Antonio Vizcaíno. 2021. “Data Management of Sensitive Human Proteomics Data: Current Practices, Recommendations, and Perspectives for the Future.” Molecular & Cellular Proteomics: MCP 20:100071. https://doi.org/10.1016/j.mcpro.2021.100071. 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
Schmidt, Tobias, Patroklos Samaras, Viktoria Dorfer, Christian Panse, Tobias Kockmann, Leon Bichmann, Bart van Puyvelde, et al. 2021. “Universal Spectrum Explorer: A Standalone (Web-)Application for Cross-Resource Spectrum Comparison.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.1c00096. Cite Download
Vos, Rutger A., Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, et al. 2020. “BioHackathon 2015: Semantics of Data for Life Sciences and Reproducible Research.” F1000Research 9:136. https://doi.org/10.12688/f1000research.18236.1. Cite Download
Bhamber, Ranjeet S., Andris Jankevics, Eric W. Deutsch, Andrew R. Jones, and Andrew W. Dowsey. 2020. “MzMLb: A Future-Proof Raw Mass Spectrometry Data Format Based on Standards-Compliant MzML and Optimized for Speed and Storage Requirements.” Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.0c00192. 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
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
Eng, Jimmy K., and Eric W. Deutsch. 2020. “Extending Comet for Global Amino Acid Variant and Post-Translational Modification Analysis Using the PSI Extended FASTA Format.” Proteomics, e1900362. https://doi.org/10.1002/pmic.201900362. Cite
Vizcaíno, Juan Antonio, Peter Kubiniok, Kevin A. Kovalchik, Qing Ma, Jérôme D. Duquette, Ian Mongrain, Eric W. Deutsch, et al. 2020. “The Human Immunopeptidome Project: A Roadmap to Predict and Treat Immune Diseases.” Molecular & Cellular Proteomics: MCP 19 (1): 31–49. https://doi.org/10.1074/mcp.R119.001743. Cite