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Eric Deutsch, PhD

Principal Scientist

ISB

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  • Biography
  • Activities
  • 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 participates in these internal and external activities:
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
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
Deutsch, E. W., Omenn, G. S., Sun, Z., Maes, M., Pernemalm, M., Palaniappan, K. K., Letunica, N., Vandenbrouck, Y., Brun, V., Tao, S.-C., Yu, X., Geyer, P. E., Ignjatovic, V., Moritz, R. L., & Schwenk, J. M. (2021). Advances and Utility of the Human Plasma Proteome. Journal of Proteome Research, 20(12), 5241–5263. https://doi.org/10.1021/acs.jproteome.1c00657 Cite
van Wijk, K. J., Leppert, T., Sun, Q., Boguraev, S. S., Sun, Z., Mendoza, L., & Deutsch, E. W. (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, C., Füllgrabe, A., Pfeuffer, J., Solovyeva, E. M., Deng, J., Moreno, P., Kamatchinathan, S., Kundu, D. J., George, N., Fexova, S., Grüning, B., Föll, M. C., Griss, J., Vaudel, M., Audain, E., Locard-Paulet, M., Turewicz, M., Eisenacher, M., Uszkoreit, J., … Perez-Riverol, Y. (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, E. W., Perez-Riverol, Y., Carver, J., Kawano, S., Mendoza, L., Van Den Bossche, T., Gabriels, R., Binz, P.-A., Pullman, B., Sun, Z., Shofstahl, J., Bittremieux, W., Mak, T. D., Klein, J., Zhu, Y., Lam, H., Vizcaíno, J. A., & Bandeira, N. (2021). Universal Spectrum Identifier for mass spectra. Nature Methods, 18(7), 768–770. https://doi.org/10.1038/s41592-021-01184-6 Cite Download
Bandeira, N., Deutsch, E. W., Kohlbacher, O., Martens, L., & Vizcaíno, J. A. (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., Sun, Z., Mascaraque, V., Pérez-Navarro, E., Vialás, V., Deutsch, E. W., Moritz, R. L., Gil, C., Martínez, J. L., & Molero, G. (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, T., Samaras, P., Dorfer, V., Panse, C., Kockmann, T., Bichmann, L., van Puyvelde, B., Perez-Riverol, Y., Deutsch, E. W., Kuster, B., & Wilhelm, M. (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, R. A., Katayama, T., Mishima, H., Kawano, S., Kawashima, S., Kim, J.-D., Moriya, Y., Tokimatsu, T., Yamaguchi, A., Yamamoto, Y., Wu, H., Amstutz, P., Antezana, E., Aoki, N. P., Arakawa, K., Bolleman, J. T., Bolton, E., Bonnal, R. J. P., Bono, H., … Takagi, T. (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, R. S., Jankevics, A., Deutsch, E. W., Jones, A. R., & Dowsey, A. W. (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, G. S., Lane, L., Overall, C. M., Cristea, I. M., Corrales, F. J., Lindskog, C., Paik, Y.-K., Van Eyk, J. E., Liu, S., Pennington, S. R., Snyder, M. P., Baker, M. S., Bandeira, N., Aebersold, R., Moritz, R. L., & Deutsch, E. W. (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, S., Nice, E. C., Deutsch, E. W., Lane, L., Omenn, G. S., Pennington, S. R., Paik, Y.-K., Overall, C. M., Corrales, F. J., Cristea, I. M., Van Eyk, J. E., Uhlén, M., Lindskog, C., Chan, D. W., Bairoch, A., Waddington, J. C., Justice, J. L., LaBaer, J., Rodriguez, H., … Baker, M. S. (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, J. K., & Deutsch, E. W. (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