Eric Deutsch, PhD

Principal Scientist

ISB

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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 participates in these internal and external activities:

Co-chair of the HUPO Proteomics Standards Initiative (PSI)
Chair of the PSI Mass Spectrometry Standards working Group (MSSWG)
Co-Chair of the Human Proteome Project (HPP) Knowledgebase Committee
Team Lead for the Trans-Proteomic Pipeline (TPP) project
Team Lead for the PeptideAtlas Project
Principal Investigator for NIH NIGMS R01 GM087221

2323737 2RQKSFR5 deutsch 1 apa 50 date year 1 1 8665 https://moritz.isbscience.org/wp-content/plugins/zotpress/

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Deutsch, E. W., Mendoza, L., & Moritz, R. L. (2025). Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.5c00092 Cite

Sun, Y., A, J., Liu, Z., Sun, R., Qian, L., Payne, S. H., Bittremieux, W., Ralser, M., Li, C., Chen, Y., Dong, Z., Perez-Riverol, Y., Khan, A., Sander, C., Aebersold, R., Vizcaíno, J. A., Krieger, J. R., Yao, J., Wen, H., … Guo, T. (2025). Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence (No. arXiv:2502.15867). arXiv. https://doi.org/10.48550/arXiv.2502.15867 Cite Download

Contreras-Moreira, B., Sharma, E., Saraf, S., Naamati, G., Gupta, P., Elser, J., Chebotarov, D., Chougule, K., Lu, Z., Wei, S., Olson, A., Tsang, I., Lodha, D., Zhou, Y., Yu, Z., Zhao, W., Zhang, J., Amberkar, S., Sue-Ob, K., … Jones, A. R. (2025). A pan-gene catalogue of Asian cultivated rice. bioRxiv. https://doi.org/10.1101/2025.02.17.638606 Cite Download

Wacholder, A., Deutsch, E. W., Kok, L. W., Dinter, J. T. van, Lee, J., Wright, J. C., Leblanc, S., Jayatissa, A. H., Jiang, K., Arefiev, I., Cao, K., Bourassa, F., Trifiro, F.-A., Bassani-Sternberg, M., Baranov, P. V., Bogaert, A., Chothani, S., Fierro-Monti, I., Fijalkowska, D., … Carvunis, A.-R. (2025). Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment. bioRxiv. https://doi.org/10.1101/2025.02.19.639069 Cite Download

Tzvetkov, J., Eyers, C. E., Eyers, P. A., Ramsbottom, K. A., Oswald, S. O., Harris, J. A., Sun, Z., Deutsch, E. W., & Jones, A. R. (2025). Searching for Sulfotyrosines (sY) in a HA(pY)STACK. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.4c00907 Cite

Tzvetkov, J., Eyers, C. E., Eyers, P. A., Ramsbottom, K. A., Oswald, S. O., Harris, J. A., Sun, Z., Deutsch, E. W., & Jones, A. R. (2025). Searching for Sulfotyrosines (sY) in a HA(pY)STACK. bioRxiv. https://doi.org/10.1101/2024.10.14.618131 Cite Download

Kalyuzhnyy, A., Eyers, P. A., Eyers, C. E., Deutsch, E. W., & Jones, A. R. (2025). Applying a conservation-based approach for predicting novel phosphorylation sites in eukaryotes and evaluating their functional relevance. bioRxiv. https://doi.org/10.1101/2025.01.09.632054 Cite Download

van Wijk, K. J., Bentolila, S., Leppert, T., Sun, Q., Sun, Z., Mendoza, L., Li, M., & Deutsch, E. W. (2024). Detection and editing of the updated Arabidopsis plastid- and mitochondrial-encoded proteomes through PeptideAtlas. Plant Physiology, 194(3), 1411–1430. https://doi.org/10.1093/plphys/kiad572 Cite Download

Gomez-Artiguez, L., Cámara-Fuentes, S. de la, Sun, Z., Hernáez, M. L., Borrajo, A., Pitarch, A., Molero, G., Monteoliva, L., Moritz, R. L., Deutsch, E. W., & Gil, C. (2024). Candida albicans a comprehensive view of the proteome. bioRxiv. https://doi.org/10.1101/2024.12.20.629377 Cite Download

Deutsch, E. W., Kok, L. W., Mudge, J. M., Ruiz-Orera, J., Fierro-Monti, I., Sun, Z., Abelin, J. G., Alba, M. M., Aspden, J. L., Bazzini, A. A., Bruford, E. A., Brunet, M. A., Calviello, L., Carr, S. A., Carvunis, A.-R., Chothani, S., Clauwaert, J., Dean, K., Faridi, P., … van Heesch, S. (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, O. J. M., Ramsbottom, K. A., Prakash, A., Sun, Z., Perez Riverol, Y., Bowler-Barnett, E., Martin, M., Fan, J., Deutsch, E. W., Vizcaíno, J. A., & Jones, A. R. (2024). Phosphorylation in the Plasmodium falciparum Proteome: A Meta-Analysis of Publicly Available Data Sets. Journal of Proteome Research, 23(12), 5326–5341. https://doi.org/10.1021/acs.jproteome.4c00418 Cite

Geyer, P. E., Hornburg, D., Pernemalm, M., Hauck, S. M., Palaniappan, K. K., Albrecht, V., Dagley, L. F., Moritz, R. L., Yu, X., Edfors, F., Vandenbrouck, Y., Mueller-Reif, J. B., Sun, Z., Brun, V., Ahadi, S., Omenn, G. S., Deutsch, E. W., & Schwenk, J. M. (2024). The Circulating Proteome─Technological Developments, Current Challenges, and Future Trends. Journal of Proteome Research, 23(12), 5279–5295. https://doi.org/10.1021/acs.jproteome.4c00586 Cite

Klein, J., Lam, H., Mak, T. D., Bittremieux, W., Perez-Riverol, Y., Gabriels, R., Shofstahl, J., Hecht, H., Binz, P.-A., Kawano, S., Van Den Bossche, T., Carver, J., Neely, B. A., Mendoza, L., Suomi, T., Claeys, T., Payne, T., Schulte, D., Sun, Z., … Deutsch, E. W. (2024). The Proteomics Standards Initiative Standardized Formats for Spectral Libraries and Fragment Ion Peak Annotations: mzSpecLib and mzPAF. Analytical Chemistry, 96(46), 18491–18501. https://doi.org/10.1021/acs.analchem.4c04091 Cite

Omenn, G. S., Orchard, S., Lane, L., Lindskog, C., Pineau, C., Overall, C. M., Budnik, B., Mudge, J. M., Packer, N. H., Weintraub, S. T., Roehrl, M. H. A., Nice, E., Guo, T., Van Eyk, J. E., Völker, U., Zhang, G., Bandeira, N., Aebersold, R., Moritz, R. L., & Deutsch, E. W. (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, N. H., & Deutsch, E. W. (2024). SpectiCal: m/z Calibration of MS2 Peptide Spectra Using Known Low Mass Ions. Journal of Proteome Research, 23(4), 1519–1530. https://doi.org/10.1021/acs.jproteome.3c00882 Cite

Omenn, G. S., Lane, L., Overall, C. M., Lindskog, C., Pineau, C., Packer, N. H., Cristea, I. M., Weintraub, S. T., Orchard, S., Roehrl, M. H. A., Nice, E., Guo, T., Van Eyk, J. E., Liu, S., Bandeira, N., Aebersold, R., Moritz, R. L., & Deutsch, E. W. (2024). The 2023 Report on the Proteome from the HUPO Human Proteome Project. Journal of Proteome Research, 23(2), 532–549. https://doi.org/10.1021/acs.jproteome.3c00591 Cite

van Wijk, K. J., Leppert, T., Sun, Z., Guzchenko, I., Debley, E., Sauermann, G., Routray, P., Mendoza, L., Sun, Q., & Deutsch, E. W. (2024). The Zea mays PeptideAtlas: A New Maize Community Resource. Journal of Proteome Research. https://doi.org/10.1021/acs.jproteome.4c00320 Cite

Ramsbottom, K. A., Prakash, A., Perez-Riverol, Y., Camacho, O. M., Sun, Z., Kundu, D. J., Bowler-Barnett, E., Martin, M., Fan, J., Chebotarov, D., McNally, K. L., Deutsch, E. W., Vizcaíno, J. A., & Jones, A. R. (2024). Meta-Analysis of Rice Phosphoproteomics Data to Understand Variation in Cell Signaling Across the Rice Pan-Genome. Journal of Proteome Research, 23(7), 2518–2531. https://doi.org/10.1021/acs.jproteome.4c00187 Cite Download

Jones, A. R., Deutsch, E. W., & Vizcaíno, J. A. (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

van Wijk, K. J., Leppert, T., Sun, Z., Kearly, A., Li, M., Mendoza, L., Guzchenko, I., Debley, E., Sauermann, G., Routray, P., Malhotra, S., Nelson, A., Sun, Q., & Deutsch, E. W. (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, K. A., Prakash, A., Riverol, Y. P., Camacho, O. M., Sun, Z., Kundu, D. J., Bowler-Barnett, E., Martin, M., Fan, J., Chebotarov, D., McNally, K. L., Deutsch, E. W., Vizcaíno, J. A., & Jones, A. R. (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

van Wijk, K. J., Bentolila, S., Leppert, T., Sun, Q., Sun, Z., Mendoza, L., Li, M., & Deutsch, E. W. (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, A. R., Wiedrick, J., Feryn, A., Maes, M., Midha, M. K., Baxter, D. H., Morrone, S. R., Prokop, T. J., Kapil, C., Hoopmann, M. R., Kusebauch, U., Deutsch, E. W., Rappaport, N., Watanabe, K., Moritz, R. L., Miller, R. A., Lapidus, J. A., & Orwoll, E. S. (2023). Proteomic changes induced by longevity-promoting interventions in mice. GeroScience. https://doi.org/10.1007/s11357-023-00917-z Cite

Prensner, J. R., Abelin, J. G., Kok, L. W., Clauser, K. R., Mudge, J. M., Ruiz-Orera, J., Bassani-Sternberg, M., Moritz, R. L., Deutsch, E. W., & van Heesch, S. (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

van Wijk, K. J., Leppert, T., Sun, Z., & Deutsch, E. W. (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), 2079–2091. https://doi.org/10.1021/acs.jproteome.3c00178 Cite

Sandmann, C.-L., Schulz, J. F., Ruiz-Orera, J., Kirchner, M., Ziehm, M., Adami, E., Marczenke, M., Christ, A., Liebe, N., Greiner, J., Schoenenberger, A., Muecke, M. B., Liang, N., Moritz, R. L., Sun, Z., Deutsch, E. W., Gotthardt, M., Mudge, J. M., Prensner, J. R., … Hubner, N. (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, A. K., Ma, C., Mendoza, L., Womack, F., Wood, E. C., Sinha, M., Acevedo, L., Kvarfordt, L. G., Peene, R. C., Liu, S., Hoffman, A. S., Roach, J. C., Deutsch, E. W., Ramsey, S. A., & Koslicki, D. (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, B. A., Dorfer, V., Martens, L., Bludau, I., Bouwmeester, R., Degroeve, S., Deutsch, E. W., Gessulat, S., Käll, L., Palczynski, P., Payne, S. H., Rehfeldt, T. G., Schmidt, T., Schwämmle, V., Uszkoreit, J., Vizcaíno, J. A., Wilhelm, M., & Palmblad, M. (2023). Toward an Integrated Machine Learning Model of a Proteomics Experiment. Journal of Proteome Research, 22(3), 681–696. https://doi.org/10.1021/acs.jproteome.2c00711 Cite Download

Rehfeldt, T. G., Gabriels, R., Bouwmeester, R., Gessulat, S., Neely, B. A., Palmblad, M., Perez-Riverol, Y., Schmidt, T., Vizcaíno, J. A., & Deutsch, E. W. (2023). ProteomicsML: An Online Platform for Community-Curated Data sets and Tutorials for Machine Learning in Proteomics. Journal of Proteome Research, 22(2), 632–636. https://doi.org/10.1021/acs.jproteome.2c00629 Cite Download

Deutsch, E. W., Mendoza, L., Shteynberg, D. D., Hoopmann, M. R., Sun, Z., Eng, J. K., & Moritz, R. L. (2023). Trans-Proteomic Pipeline: Robust Mass Spectrometry-Based Proteomics Data Analysis Suite. Journal of Proteome Research, 22(2), 615–624. https://doi.org/10.1021/acs.jproteome.2c00624 Cite

Deutsch, E. W., Vizcaíno, J. A., Jones, A. R., Binz, P.-A., Lam, H., Klein, J., Bittremieux, W., Perez-Riverol, Y., Tabb, D. L., Walzer, M., Ricard-Blum, S., Hermjakob, H., Neumann, S., Mak, T. D., Kawano, S., Mendoza, L., Van Den Bossche, T., Gabriels, R., Bandeira, N., … Orchard, S. E. (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, E. W., Bandeira, N., Perez-Riverol, Y., Sharma, V., Carver, J. J., Mendoza, L., Kundu, D. J., Wang, S., Bandla, C., Kamatchinathan, S., Hewapathirana, S., Pullman, B. S., Wertz, J., Sun, Z., Kawano, S., Okuda, S., Watanabe, Y., MacLean, B., MacCoss, M. J., … Vizcaíno, J. A. (2022). The ProteomeXchange consortium at 10 years: 2023 update. Nucleic Acids Research, gkac1040. https://doi.org/10.1093/nar/gkac1040 Cite Download Download

Omenn, G. S., Lane, L., Overall, C. M., Pineau, C., Packer, N. H., Cristea, I. M., Lindskog, C., Weintraub, S. T., Orchard, S., Roehrl, M. H. A., Nice, E., Liu, S., Bandeira, N., Chen, Y.-J., Guo, T., Aebersold, R., Moritz, R. L., & Deutsch, E. W. (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, E., Mendoza, L., Shteynberg, D., Hoopmann, M., Sun, Z., Eng, J., & Moritz, R. (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, A. K., Ma, C., Mendoza, L., Womack, F., Wood, E. C., Sinha, M., Acevedo, L., Kvarfordt, L. G., Peene, R. C., Liu, S., Hoffman, A. S., Roach, J. C., Deutsch, E. W., Ramsey, S. A., & Koslicki, D. (2022). ARAX: a graph-based modular reasoning tool for translational biomedicine. bioRxiv. https://doi.org/10.1101/2022.08.12.503810 Cite Download

Rehfeldt, T., Gabriels, R., Bouwmeester, R., Gessulat, S., Neely, B., Palmblad, M., Perez-Riverol, Y., Schmidt, T., Vizcaíno, J. A., & Deutsch, E. (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, A., Deutsch, E., & Vizcaino, J. A. (2022). Is DIA proteomics data FAIR? Current data sharing practices, available bioinformatics infrastructure and recommendations for the future – Jones – PROTEOMICS – Wiley Online Library. https://analyticalsciencejournals.onlinelibrary.wiley.com/doi/10.1002/pmic.202200014 Cite

Wood, E. C., Glen, A. K., Kvarfordt, L. G., Womack, F., Acevedo, L., Yoon, T. S., Ma, C., Flores, V., Sinha, M., Chodpathumwan, Y., Termehchy, A., Roach, J. C., Mendoza, L., Hoffman, A. S., Deutsch, E. W., Koslicki, D., & Ramsey, S. A. (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, J. M., Ruiz-Orera, J., Prensner, J. R., Brunet, M. A., Calvet, F., Jungreis, I., Gonzalez, J. M., Magrane, M., Martinez, T. F., Schulz, J. F., Yang, Y. T., Albà, M. M., Aspden, J. L., Baranov, P. V., Bazzini, A. A., Bruford, E., Martin, M. J., Calviello, L., Carvunis, A.-R., … van Heesch, S. (2022). Standardized annotation of translated open reading frames. Nature Biotechnology, 40(7), 994–999. https://doi.org/10.1038/s41587-022-01369-0 Cite Download

Ramsbottom, K. A., Prakash, A., Riverol, Y. P., Camacho, O. M., Martin, M.-J., Vizcaíno, J. A., Deutsch, E. W., & Jones, A. R. (2022). Method for Independent Estimation of the False Localization Rate for Phosphoproteomics. Journal of Proteome Research, 21(7), 1603–1615. https://doi.org/10.1021/acs.jproteome.1c00827 Cite

Luo, X., Bittremieux, W., Griss, J., Deutsch, E. W., Sachsenberg, T., Levitsky, L. I., Ivanov, M. V., Bubis, J. A., Gabriels, R., Webel, H., Sanchez, A., Bai, M., Käll, L., & Perez-Riverol, Y. (2022). A Comprehensive Evaluation of Consensus Spectrum Generation Methods in Proteomics. Journal of Proteome Research, 21(6), 1566–1574. https://doi.org/10.1021/acs.jproteome.2c00069 Cite Download

Kalyuzhnyy, A., Eyers, P. A., Eyers, C. E., Bowler-Barnett, E., Martin, M. J., Sun, Z., Deutsch, E. W., & Jones, A. R. (2022). Profiling the Human Phosphoproteome to Estimate the True Extent of Protein Phosphorylation. Journal of Proteome Research, 21(6), 1510–1524. https://doi.org/10.1021/acs.jproteome.2c00131 Cite Download

LeDuc, R. D., Deutsch, E. W., Binz, P.-A., Fellers, R. T., Cesnik, A. J., Klein, J. A., Van Den Bossche, T., Gabriels, R., Yalavarthi, A., Perez-Riverol, Y., Carver, J., Bittremieux, W., Kawano, S., Pullman, B., Bandeira, N., Kelleher, N. L., Thomas, P. M., & Vizcaíno, J. A. (2022). Proteomics Standards Initiative’s ProForma 2.0: Unifying the Encoding of Proteoforms and Peptidoforms. Journal of Proteome Research, 21(4), 1189–1195. https://doi.org/10.1021/acs.jproteome.1c00771 Cite

Omenn, G. S., Lane, L., Overall, C. M., Paik, Y.-K., Cristea, I. M., Corrales, F. J., Lindskog, C., Weintraub, S., Roehrl, M. H. A., Liu, S., Bandeira, N., Srivastava, S., Chen, Y.-J., Aebersold, R., Moritz, R. L., & Deutsch, E. W. (2021). Progress Identifying and Analyzing the Human Proteome: 2021 Metrics from the HUPO Human Proteome Project. Journal of Proteome Research, 20(12), 5227–5240. https://doi.org/10.1021/acs.jproteome.1c00590 Cite