Eric Deutsch, PhD

Senior Research Scientist

Moritz Lab

Eric Deutsch

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 Pipelineproject, 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.

Spellman, P. T., M. Miller, J. Stewart, C. Troup, U. Sarkans, S. Chervitz, D. Bernhart, et al. 2002. “Design and Implementation of Microarray Gene Expression Markup Language (MAGE-ML).” Genome Biol 3 (9): RESEARCH0046. Cite
Taylor, C. F., N. W. Paton, K. L. Garwood, P. D. Kirby, D. A. Stead, Z. Yin, E. W. Deutsch, et al. 2003. “A Systematic Approach to Modeling, Capturing, and Disseminating Proteomics Experimental Data.” Nat Biotechnol 21 (3): 247–54. Cite
Janer, M., D. M. Friedrichsen, J. L. Stanford, M. D. Badzioch, S. Kolb, K. Deutsch, M. A. Peters, et al. 2003. “Genomic Scan of 254 Hereditary Prostate Cancer Families.” Prostate 57 (4): 309–19. Cite
Bonneau, R., N. S. Baliga, E. W. Deutsch, P. Shannon, and L. Hood. 2004. “Comprehensive de Novo Structure Prediction in a Systems-Biology Context for the Archaea Halobacterium Sp. NRC-1.” Genome Biol 5 (8): R52. Cite
Goo, Y. A., J. Roach, G. Glusman, N. S. Baliga, K. Deutsch, M. Pan, S. Kennedy, S. DasSarma, W. V. Ng, and L. Hood. 2004. “Low-Pass Sequencing for Microbial Comparative Genomics.” BMC Genomics 5 (1): 3. Cite
Friedrichsen, D. M., J. L. Stanford, S. D. Isaacs, M. Janer, B. L. Chang, K. Deutsch, E. Gillanders, et al. 2004. “Identification of a Prostate Cancer Susceptibility Locus on Chromosome 7q11-21 in Jewish Families.” Proc Natl Acad Sci U S A 101 (7): 1939–44. Cite
Yan, W., H. Lee, E. W. Deutsch, C. A. Lazaro, W. Tang, E. Chen, N. Fausto, M. G. Katze, and R. Aebersold. 2004. “A Dataset of Human Liver Proteins Identified by Protein Profiling via Isotope-Coded Affinity Tag (ICAT) and Tandem Mass Spectrometry.” Mol Cell Proteomics 3 (10): 1039–41. Cite
Baliga, N. S., R. Bonneau, M. T. Facciotti, M. Pan, G. Glusman, E. W. Deutsch, P. Shannon, et al. 2004. “Genome Sequence of Haloarcula Marismortui: A Halophilic Archaeon from the Dead Sea.” Genome Res 14 (11): 2221–34. Cite
Pedrioli, P. G., J. K. Eng, R. Hubley, M. Vogelzang, E. W. Deutsch, B. Raught, B. Pratt, et al. 2004. “A Common Open Representation of Mass Spectrometry Data and Its Application to Proteomics Research.” Nat Biotechnol 22 (11): 1459–66. Cite
Desiere, F., E. W. Deutsch, A. I. Nesvizhskii, P. Mallick, N. L. King, J. K. Eng, A. Aderem, et al. 2005. “Integration with the Human Genome of Peptide Sequences Obtained by High-Throughput Mass Spectrometry.” Genome Biol 6 (1): R9. Cite
Deutsch, E. W., J. K. Eng, H. Zhang, N. L. King, A. I. Nesvizhskii, B. Lin, H. Lee, E. C. Yi, R. Ossola, and R. Aebersold. 2005. “Human Plasma PeptideAtlas.” Proteomics 5 (13): 3497–3500. Cite
Xu, J., L. Dimitrov, B. L. Chang, T. S. Adams, A. R. Turner, D. A. Meyers, R. A. Eeles, et al. 2005. “A Combined Genomewide Linkage Scan of 1,233 Families for Prostate Cancer-Susceptibility Genes Conducted by the International Consortium for Prostate Cancer Genetics.” Am J Hum Genet 77 (2): 219–29. Cite
Chen, S. S., E. W. Deutsch, E. C. Yi, X. J. Li, D. R. Goodlett, and R. Aebersold. 2005. “Improving Mass and Liquid Chromatography Based Identification of Proteins Using Bayesian Scoring.” J Proteome Res 4 (6): 2174–84. Cite
Marzolf, B., E. W. Deutsch, P. Moss, D. Campbell, M. H. Johnson, and T. Galitski. 2006. “SBEAMS-Microarray: Database Software Supporting Genomic Expression Analyses for Systems Biology.” BMC Bioinformatics 7: 286. Cite
Deutsch, E. W., C. A. Ball, G. S. Bova, A. Brazma, R. E. Bumgarner, D. Campbell, H. C. Causton, et al. 2006. “Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).” OMICS 10 (2): 205–8. Cite
King, N. L., E. W. Deutsch, J. Ranish, A. I. Nesvizhskii, J. S. Eddes, P. Mallick, J. Eng, et al. 2006. “Analysis of the Saccharomyces Cerevisiae Proteome with PeptideAtlas.” Genome Biol 7 (11): R106. Cite
Desiere, F., E. W. Deutsch, N. L. King, A. I. Nesvizhskii, P. Mallick, J. Eng, S. Chen, J. Eddes, S. N. Loevenich, and R. Aebersold. 2006. “The PeptideAtlas Project.” Nucleic Acids Res 34 (Database issue): D655-8. Cite
Stanford, J. L., S. K. McDonnell, D. M. Friedrichsen, E. E. Carlson, S. Kolb, K. Deutsch, M. Janer, L. Hood, E. A. Ostrander, and D. J. Schaid. 2006. “Prostate Cancer and Genetic Susceptibility: A Genome Scan Incorporating Disease Aggressiveness.” Prostate 66 (3): 317–25. Cite
Roach, J., K. Deutsch, S. Li, A. F. Siegel, L. M. Bekris, D. C. Einhaus, C. M. Sheridan, et al. 2006. “Genetic Mapping at 3-Kilobase Resolution Reveals Inositol 1,4,5-Triphosphate Receptor 3 as a Risk Factor for Type 1 Diabetes in Sweden.” Am J Hum Genet 79 (4): 614–27. Cite
Schaid, D. J., S. K. McDonnell, K. E. Zarfas, J. M. Cunningham, S. Hebbring, S. N. Thibodeau, R. A. Eeles, et al. 2006. “Pooled Genome Linkage Scan of Aggressive Prostate Cancer: Results from the International Consortium for Prostate Cancer Genetics.” Hum Genet 120 (4): 471–85. Cite
Pascal, L. E., E. W. Deutsch, D. S. Campbell, M. Korb, L. D. True, and A. Y. Liu. 2007. “The Urologic Epithelial Stem Cell Database (UESC) - a Web Tool for Cell Type-Specific Gene Expression and Immunohistochemistry Images of the Prostate and Bladder.” BMC Urol 7: 19. Cite
Lam, H., E. W. Deutsch, J. S. Eddes, J. K. Eng, N. King, S. E. Stein, and R. Aebersold. 2007. “Development and Validation of a Spectral Library Searching Method for Peptide Identification from MS/MS.” Proteomics 7 (5): 655–67. Cite
Iyer, S., K. Deutsch, X. Yan, and B. Lin. 2007. “Batch RNAi Selector: A Standalone Program to Predict Specific SiRNA Candidates in Batches with Enhanced Sensitivity.” Comput Methods Programs Biomed 85 (3): 203–9. Cite
Pierce, B. L., D. M. Friedrichsen-Karyadi, L. McIntosh, K. Deutsch, L. Hood, E. A. Ostrander, M. A. Austin, and J. L. Stanford. 2007. “Genomic Scan of 12 Hereditary Prostate Cancer Families Having an Occurrence of Pancreas Cancer.” Prostate 67 (4): 410–15. Cite
Brunner, E., C. H. Ahrens, S. Mohanty, H. Baetschmann, S. Loevenich, F. Potthast, E. W. Deutsch, et al. 2007. “A High-Quality Catalog of the Drosophila Melanogaster Proteome.” Nat Biotechnol 25 (5): 576–83. Cite
Johanneson, B., K. Deutsch, L. McIntosh, D. M. Friedrichsen-Karyadi, M. Janer, E. M. Kwon, L. Iwasaki, L. Hood, E. A. Ostrander, and J. L. Stanford. 2007. “Suggestive Genetic Linkage to Chromosome 11p11.2-Q12.2 in Hereditary Prostate Cancer Families with Primary Kidney Cancer.” Prostate 67 (7): 732–42. Cite
Camp, N. J., L. A. Cannon-Albright, J. M. Farnham, A. B. Baffoe-Bonnie, A. George, I. Powell, J. E. Bailey-Wilson, et al. 2007. “Compelling Evidence for a Prostate Cancer Gene at 22q12.3 by the International Consortium for Prostate Cancer Genetics.” Hum Mol Genet 16 (11): 1271–78. Cite
Schaid, D. J., J. L. Stanford, S. K. McDonnell, M. Suuriniemi, L. McIntosh, D. M. Karyadi, E. E. Carlson, et al. 2007. “Genome-Wide Linkage Scan of Prostate Cancer Gleason Score and Confirmation of Chromosome 19q.” Hum Genet 121 (6): 729–35. Cite
Taylor, C. F., N. W. Paton, K. S. Lilley, P. A. Binz, Jr Julian, A. R. Jones, W. Zhu, et al. 2007. “The Minimum Information about a Proteomics Experiment (MIAPE).” Nat Biotechnol 25 (8): 887–93. Cite
Shin, J. H., M. Janer, B. McNeney, S. Blay, K. Deutsch, C. B. Sanjeevi, I. Kockum, et al. 2007. “IA-2 Autoantibodies in Incident Type I Diabetes Patients Are Associated with a Polyadenylation Signal Polymorphism in GIMAP5.” Genes Immun 8 (6): 503–12. Cite
Pascal, L. E., L. D. True, D. S. Campbell, E. W. Deutsch, M. Risk, I. M. Coleman, L. J. Eichner, P. S. Nelson, and A. Y. Liu. 2008. “Correlation of MRNA and Protein Levels: Cell Type-Specific Gene Expression of Cluster Designation Antigens in the Prostate.” BMC Genomics 9: 246. Cite
Zhang, Q., R. Menon, E. W. Deutsch, S. J. Pitteri, V. M. Faca, H. Wang, L. F. Newcomb, et al. 2008. “A Mouse Plasma Peptide Atlas as a Resource for Disease Proteomics.” Genome Biol 9 (6): R93. Cite
Mathivanan, S., M. Ahmed, N. G. Ahn, H. Alexandre, R. Amanchy, P. C. Andrews, J. S. Bader, et al. 2008. “Human Proteinpedia Enables Sharing of Human Protein Data.” Nat Biotechnol 26 (2): 164–67. Cite
Johanneson, B., S. K. McDonnell, D. M. Karyadi, S. J. Hebbring, L. Wang, K. Deutsch, L. McIntosh, et al. 2008. “Fine Mapping of Familial Prostate Cancer Families Narrows the Interval for a Susceptibility Locus on Chromosome 22q12.3 to 1.36 Mb.” Hum Genet 123 (1): 65–75. Cite
Deutsch, E. W., C. A. Ball, J. J. Berman, G. S. Bova, A. Brazma, R. E. Bumgarner, D. Campbell, et al. 2008. “Minimum Information Specification for in Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE).” Nat Biotechnol 26 (3): 305–12. Cite
Deutsch, E. W., H. Lam, and R. Aebersold. 2008. “Data Analysis and Bioinformatics Tools for Tandem Mass Spectrometry in Proteomics.” Physiol Genomics 33 (1): 18–25. Cite
Deutsch, E. W., H. Lam, and R. Aebersold. 2008. “PeptideAtlas: A Resource for Target Selection for Emerging Targeted Proteomics Workflows.” EMBO Rep 9 (5): 429–34. Cite
Lange, V., J. A. Malmstrom, J. Didion, N. L. King, B. P. Johansson, J. Schafer, J. Rameseder, et al. 2008. “Targeted Quantitative Analysis of Streptococcus Pyogenes Virulence Factors by Multiple Reaction Monitoring.” Mol Cell Proteomics 7 (8): 1489–1500. Cite
Taylor, C. F., P. A. Binz, R. Aebersold, M. Affolter, R. Barkovich, E. W. Deutsch, D. M. Horn, et al. 2008. “Guidelines for Reporting the Use of Mass Spectrometry in Proteomics.” Nat Biotechnol 26 (8): 860–61. Cite
Taylor, C. F., D. Field, S. A. Sansone, J. Aerts, R. Apweiler, M. Ashburner, C. A. Ball, et al. 2008. “Promoting Coherent Minimum Reporting Guidelines for Biological and Biomedical Investigations: The MIBBI Project.” Nat Biotechnol 26 (8): 889–96. Cite
Van, P. T., A. K. Schmid, N. L. King, A. Kaur, M. Pan, K. Whitehead, T. Koide, et al. 2008. “Halobacterium Salinarum NRC-1 PeptideAtlas: Toward Strategies for Targeted Proteomics and Improved Proteome Coverage.” J Proteome Res 7 (9): 3755–64. Cite
Lam, H., E. W. Deutsch, J. S. Eddes, J. K. Eng, S. E. Stein, and R. Aebersold. 2008. “Building Consensus Spectral Libraries for Peptide Identification in Proteomics.” Nat Methods 5 (10): 873–75. Cite
Picotti, P., H. Lam, D. Campbell, E. W. Deutsch, H. Mirzaei, J. Ranish, B. Domon, and R. Aebersold. 2008. “A Database of Mass Spectrometric Assays for the Yeast Proteome.” Nat Methods 5 (11): 913–14. Cite
Koide, T., D. J. Reiss, J. C. Bare, W. L. Pang, M. T. Facciotti, A. K. Schmid, M. Pan, et al. 2009. “Prevalence of Transcription Promoters within Archaeal Operons and Coding Sequences.” Mol Syst Biol 5: 285. Cite
Loevenich, S. N., E. Brunner, N. L. King, E. W. Deutsch, S. E. Stein, Consortium FlyBase, R. Aebersold, and E. Hafen. 2009. “The Drosophila Melanogaster PeptideAtlas Facilitates the Use of Peptide Data for Improved Fly Proteomics and Genome Annotation.” BMC Bioinformatics 10: 59. Cite
Stanford, J. L., L. M. Fitzgerald, S. K. McDonnell, E. E. Carlson, L. M. McIntosh, K. Deutsch, L. Hood, E. A. Ostrander, and D. J. Schaid. 2009. “Dense Genome-Wide SNP Linkage Scan in 301 Hereditary Prostate Cancer Families Identifies Multiple Regions with Suggestive Evidence for Linkage.” Hum Mol Genet 18 (10): 1839–48. Cite
Bell, A. W., E. W. Deutsch, C. E. Au, R. E. Kearney, R. Beavis, S. Sechi, T. Nilsson, and J. J. Bergeron. 2009. “A HUPO Test Sample Study Reveals Common Problems in Mass Spectrometry-Based Proteomics.” Nat Methods 6 (6): 423–30. Cite
Malmstrom, J., M. Beck, A. Schmidt, V. Lange, E. W. Deutsch, and R. Aebersold. 2009. “Proteome-Wide Cellular Protein Concentrations of the Human Pathogen Leptospira Interrogans.” Nature 460 (7256): 762–65. Cite
Sherwood, C. A., A. Eastham, L. W. Lee, A. Peterson, J. K. Eng, D. Shteynberg, L. Mendoza, et al. 2009. “MaRiMba: A Software Application for Spectral Library-Based MRM Transition List Assembly.” J Proteome Res 8 (10): 4396–4405. Cite
Beck, M., J. A. Malmstrom, V. Lange, A. Schmidt, E. W. Deutsch, and R. Aebersold. 2009. “Visual Proteomics of the Human Pathogen Leptospira Interrogans.” Nat Methods 6 (11): 817–23. Cite