Eric Deutsch

Senior Research Scientist

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:

Eng, Jimmy K., Ashley L. McCormack, and John R. Yates. 1994. “An Approach to Correlate Tandem Mass Spectral Data of Peptides with Amino Acid Sequences in a Protein Database.” Journal of the American Society for Mass Spectrometry 5(11): 976–89. (July 19, 2019). Cite Download
Perkins, D. N., D. J. Pappin, D. M. Creasy, and J. S. Cottrell. 1999. “Probability-Based Protein Identification by Searching Sequence Databases Using Mass Spectrometry Data.” Electrophoresis 20(18): 3551–67. Cite
Fredriksson, Simon et al. 2002. “Protein Detection Using Proximity-Dependent DNA Ligation Assays.” Nature Biotechnology 20(5): 473–77. Cite
Hanash, Sam, and Julio E. Celis. 2002. “The Human Proteome Organization: A Mission to Advance Proteome Knowledge.” Molecular & cellular proteomics: MCP 1(6): 413–14. Cite
Anderson, N. Leigh, and Norman G. Anderson. 2002. “The Human Plasma Proteome: History, Character, and Diagnostic Prospects.” Molecular & cellular proteomics: MCP 1(11): 845–67. Cite
Adkins, Joshua N. et al. 2002. “Toward a Human Blood Serum Proteome: Analysis by Multidimensional Separation Coupled with Mass Spectrometry.” Molecular & cellular proteomics: MCP 1(12): 947–55. Cite
Lundblad, R. 2003. “Considerations for the Use of Blood Plasma and Serum for Proteomic Analysis.” The Internet Journal of Genomics and Proteomics 1(2): 8. Cite Download
Pieper, Rembert et al. 2003. “Multi-Component Immunoaffinity Subtraction Chromatography: An Innovative Step towards a Comprehensive Survey of the Human Plasma Proteome.” Proteomics 3(4): 422–32. Cite
Lathrop, Julia Tait, N. Leigh Anderson, Norman G. Anderson, and David J. Hammond. 2003. “Therapeutic Potential of the Plasma Proteome.” Current Opinion in Molecular Therapeutics 5(3): 250–57. Cite
Pieper, Rembert et al. 2003. “The Human Serum Proteome: Display of Nearly 3700 Chromatographically Separated Protein Spots on Two-Dimensional Electrophoresis Gels and Identification of 325 Distinct Proteins.” Proteomics 3(7): 1345–64. Cite
Tirumalai, Radhakrishna S. et al. 2003. “Characterization of the Low Molecular Weight Human Serum Proteome.” Molecular & cellular proteomics: MCP 2(10): 1096–1103. Cite Download
Rosenblatt, Kevin P. et al. 2004. “Serum Proteomics in Cancer Diagnosis and Management.” Annual Review of Medicine 55: 97–112. Cite
Anderson, N. Leigh et al. 2004. “Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA).” Journal of Proteome Research 3(2): 235–44. Cite
Irizarry, Michael C. 2004. “Biomarkers of Alzheimer Disease in Plasma.” NeuroRx: The Journal of the American Society for Experimental NeuroTherapeutics 1(2): 226–34. Cite Download
Ornstein, David K., and Emmanuel F. Petricoin. 2004. “Proteomics to Diagnose Human Tumors and Provide Prognostic Information.” Oncology (Williston Park, N.Y.) 18(4): 521–29; discussion 529-532. Cite
Anderson, N. Leigh et al. 2004. “The Human Plasma Proteome: A Nonredundant List Developed by Combination of Four Separate Sources.” Molecular & cellular proteomics: MCP 3(4): 311–26. Cite Download
Li, Jinong et al. 2004. “Detection of Prostate Cancer Using Serum Proteomics Pattern in a Histologically Confirmed Population.” The Journal of Urology 171(5): 1782–87. Cite
“Circulating Nucleic Acids in Plasma/Serum III and Serum Proteomics. Proceedings of the Third International Symposium. November 9-12, 2003. Santa Monica, California, USA.” 2004. Annals of the New York Academy of Sciences 1022: xi; 1–322. Cite
Gerton, G. L. et al. 2004. “A Serum Proteomics Approach to the Diagnosis of Ectopic Pregnancy.” Annals of the New York Academy of Sciences 1022: 306–16. Cite
Gullberg, Mats et al. 2004. “Cytokine Detection by Antibody-Based Proximity Ligation.” Proceedings of the National Academy of Sciences of the United States of America 101(22): 8420–24. Cite Download Download
Craig, Robertson, and Ronald C. Beavis. 2004. “TANDEM: Matching Proteins with Tandem Mass Spectra.” Bioinformatics (Oxford, England) 20(9): 1466–67. Cite Download
Meric-Bernstam, Funda. 2004. “Serum Proteomics for BRCA1-Associated Breast Cancer.” Annals of Surgical Oncology 11(10): 883–84. Cite
Li, Xue-hua, Xin Li, Shou-jun Xu, and Yan-qing Ding. 2004. “[Establishment and evaluation of the method for removing albumin and IgG in serum proteomics].” Di 1 jun yi da xue xue bao = Academic journal of the first medical college of PLA 24(11): 1233–35. Cite
Figg, William D. et al. 2004. “Gleason Score and Pretreatment Prostate-Specific Antigen in Survival among Patients with Stage D2 Prostate Cancer.” World Journal of Urology 22(6): 425–30. Cite
de Noo, M. E., G. J. Liefers, and R. a. E. M. Tollenaar. 2005. “Translational Research in Prognostic Profiling in Colorectal Cancer.” Digestive Surgery 22(4): 276–81. Cite
Tripodi, Armando et al. 2005. “Evidence of Normal Thrombin Generation in Cirrhosis despite Abnormal Conventional Coagulation Tests.” Hepatology 41(3): 553–58. (June 27, 2019). Cite Download
Ransohoff, David F. 2005. “Lessons from Controversy: Ovarian Cancer Screening and Serum Proteomics.” Journal of the National Cancer Institute 97(4): 315–19. Cite Download
Ouyang, Daniel L., Joseph J. Chen, Robert H. Getzenberg, and Robert E. Schoen. 2005. “Noninvasive Testing for Colorectal Cancer: A Review.” The American Journal of Gastroenterology 100(6): 1393–1403. Cite
Murphy, Vanessa E. et al. 2005. “The Effect of Maternal Asthma on Placental and Cord Blood Protein Profiles.” Journal of the Society for Gynecologic Investigation 12(5): 349–55. Cite
Haab, Brian B. et al. 2005. “Immunoassay and Antibody Microarray Analysis of the HUPO Plasma Proteome Project Reference Specimens: Systematic Variation between Sample Types and Calibration of Mass Spectrometry Data.” Proteomics 5(13): 3278–91. Cite
Misek, David E. et al. 2005. “A Wide Range of Protein Isoforms in Serum and Plasma Uncovered by a Quantitative Intact Protein Analysis System.” Proteomics 5(13): 3343–52. Cite
Deutsch, Eric W. et al. 2005. “Human Plasma PeptideAtlas.” Proteomics 5(13): 3497–3500. Cite
Omenn, Gilbert S. et al. 2005. “Overview of the HUPO Plasma Proteome Project: Results from the Pilot Phase with 35 Collaborating Laboratories and Multiple Analytical Groups, Generating a Core Dataset of 3020 Proteins and a Publicly-Available Database.” Proteomics 5(13): 3226–45. Cite Download Download
Keller, Andrew et al. 2005. “A Uniform Proteomics MS/MS Analysis Platform Utilizing Open XML File Formats.” Molecular Systems Biology 1(1): E1–8. (January 23, 2019). Cite Download
Xu, Ronghui, and Anthony Gamst. 2005. “Re: Lessons from Controversy: Ovarian Cancer Screening and Serum Proteomics.” Journal of the National Cancer Institute 97(16): 1226; author reply 1227. Cite Download
Thulasiraman, Vanitha et al. 2005. “Reduction of the Concentration Difference of Proteins in Biological Liquids Using a Library of Combinatorial Ligands.” Electrophoresis 26(18): 3561–71. Cite
Musselman, Ian, and David W. Speicher. 2005. “Human Serum and Plasma Proteomics.” Current Protocols in Protein Science Chapter 24: Unit 24.1. Cite
King, Nichole L. et al. 2006. “Analysis of the Saccharomyces Cerevisiae Proteome with PeptideAtlas.” Genome Biology 7(11): R106. Cite Download
Desiere, F. 2006. “The PeptideAtlas Project.” Nucleic Acids Research 34(90001): D655–58. (January 23, 2019). Cite Download
Goufman, E. I. et al. 2006. “Two-Dimensional Electrophoretic Proteome Study of Serum Thermostable Fraction from Patients with Various Tumor Conditions.” Biochemistry. Biokhimiia 71(4): 354–60. Cite
Anderson, Leigh, and Christie L. Hunter. 2006. “Quantitative Mass Spectrometric Multiple Reaction Monitoring Assays for Major Plasma Proteins.” Molecular & cellular proteomics: MCP 5(4): 573–88. Cite Download Download
Albitar, Maher et al. 2006. “Proteomic-Based Prediction of Clinical Behavior in Adult Acute Lymphoblastic Leukemia.” Cancer 106(7): 1587–94. Cite Download
Kawada, Norifumi. 2006. “Cancer Serum Proteomics in Gastroenterology.” Gastroenterology 130(6): 1917–19. Cite
Okano, Tetsuya et al. 2006. “Plasma Proteomics of Lung Cancer by a Linkage of Multi-Dimensional Liquid Chromatography and Two-Dimensional Difference Gel Electrophoresis.” Proteomics 6(13): 3938–48. Cite
Zhou, Liang et al. 2006. “Detection of Hypopharyngeal Squamous Cell Carcinoma Using Serum Proteomics.” Acta Oto-Laryngologica 126(8): 853–60. Cite
Souchelnytskyi, Serhiy et al. 2006. “Proteomics Success Story. Towards Early Detection of Breast and Ovarian Cancer: Plasma Proteomics as a Tool to Find Novel Markers.” Proteomics 6 Suppl 2: 65–68. Cite
Barker, Peter E. et al. 2006. “Standards for Plasma and Serum Proteomics in Early Cancer Detection: A Needs Assessment Report from the National Institute of Standards and Technology--National Cancer Institute Standards, Methods, Assays, Reagents and Technologies Workshop, August 18-19, 2005.” Clinical Chemistry 52(9): 1669–74. Cite Download
Clemente, Luis Felipe et al. 2018. “Identification of the Missing Protein Hyaluronan Synthase 1 in Human Mesenchymal Stem Cells Derived from Adipose Tissue or Umbilical Cord.” Journal of Proteome Research. Cite
Macron, Charlotte, Lydie Lane, Antonio Núñez Galindo, and Loïc Dayon. 2018. “Identification of Missing Proteins in Normal Human Cerebrospinal Fluid.” Journal of Proteome Research. Cite
Hwang, Heeyoun et al. 2018. “Identification of Missing Proteins in Human Olfactory Epithelial Tissue by Liquid Chromatography-Tandem Mass Spectrometry.” Journal of Proteome Research. Cite
Yu, Kun-Hsing et al. 2018. “A Cloud-Based Metabolite and Chemical Prioritization System for the Biology/Disease-Driven Human Proteome Project.” Journal of Proteome Research. Cite
Omenn, Gilbert S. et al. 2018. “Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project.” Journal of Proteome Research. Cite
Wang, Jie et al. 2018. “Integrated Dissection of Cysteine Oxidative Post-Translational Modification Proteome During Cardiac Hypertrophy.” Journal of Proteome Research. Cite
Macron, Charlotte, Lydie Lane, Antonio Núñez Galindo, and Loïc Dayon. 2018. “Deep Dive on the Proteome of Human Cerebrospinal Fluid: A Valuable Data Resource for Biomarker Discovery and Missing Protein Identification.” Journal of Proteome Research. Cite
Melaine, Nathalie et al. 2018. “Deciphering the Dark Proteome: Use of the Testis and Characterization of Two Dark Proteins.” Journal of Proteome Research. Cite
Sajulga, Ray et al. 2018. “Bridging the Chromosome-Centric and Biology/Disease-Driven Human Proteome Projects: Accessible and Automated Tools for Interpreting the Biological and Pathological Impact of Protein Sequence Variants Detected via Proteogenomics.” Journal of Proteome Research. Cite
Robin, Thibault et al. 2018. “Large-Scale Reanalysis of Publicly Available HeLa Cell Proteomics Data in the Context of the Human Proteome Project.” Journal of Proteome Research. Cite
Duek, Paula, Alain Gateau, Amos Bairoch, and Lydie Lane. 2018. “Exploring the Uncharacterized Human Proteome Using NeXtProt.” Journal of Proteome Research. Cite
Weldemariam, Mehari Muuz et al. 2018. “Subcellular Proteome Landscape of Human Embryonic Stem Cells Revealed Missing Membrane Proteins.” Journal of Proteome Research. Cite
Zhang, Chengxin, Xiaoqiong Wei, Gilbert S. Omenn, and Yang Zhang. 2018. “Structure and Protein Interaction-Based Gene Ontology Annotations Reveal Likely Functions of Uncharacterized Proteins on Human Chromosome 17.” Journal of Proteome Research. Cite
Boersema, Paul J. et al. 2018. “Biology/Disease-Driven Initiative on Protein-Aggregation Diseases of the Human Proteome Project: Goals and Progress to Date.” Journal of Proteome Research. Cite
Mendoza, Luis et al. 2018. “Flexible and Fast Mapping of Peptides to a Proteome with ProteoMapper.” Journal of Proteome Research. Cite
Sjöstedt, Evelina et al. 2018. “Integration of Transcriptomics and Antibody-Based Proteomics for Exploration of Proteins Expressed in Specialized Tissues.” Journal of Proteome Research. Cite
Deutsch, Eric W. et al. 2018. “Expanding the Use of Spectral Libraries in Proteomics.” Journal of Proteome Research. Cite
Paik, Young-Ki et al. 2018. “Launching the C-HPP Pilot Project for Functional Characterization of Identified Proteins with No Known Function.” Journal of Proteome Research. Cite
He, Cuitong et al. 2018. “Digging for Missing Proteins Using Low-Molecular-Weight Protein Enrichment and a ‘Mirror Protease’ Strategy.” Journal of Proteome Research. Cite
Naryzhny, Stanislav N. et al. 2018. “Next Steps on in Silico 2DE Analyses of Chromosome 18 Proteoforms.” Journal of Proteome Research. Cite
Sun, Jinshuai et al. 2018. “Multi-Proteases Combined with High-PH Reverse-Phase Separation Strategy Verified Fourteen Missing Proteins in Human Testis Tissue.” Journal of Proteome Research. Cite
Siddiqui, Omer, Hongjiu Zhang, Yuanfang Guan, and Gilbert S. Omenn. 2018. “Chromosome 17 Missing Proteins: Recent Progress and Future Directions as Part of the Next-50MP Challenge.” Journal of Proteome Research. Cite
Ronci, Maurizio et al. 2018. “Sequential Fractionation Strategy Identifies Three Missing Proteins in the Mitochondrial Proteome of Commonly Used Cell Lines.” Journal of Proteome Research. Cite
Jeong, Seul-Ki, Chae-Yeon Kim, and Young-Ki Paik. 2018. “ASV-ID, a Proteogenomic Workflow to Predict Candidate Protein Isoforms Based on Transcript Evidence.” Journal of Proteome Research. Cite
Monti, Chiara, Lydie Lane, Mauro Fasano, and Tiziana Alberio. 2018. “Update of the Functional Mitochondrial Human Proteome Network.” Journal of Proteome Research. Cite
Lau, Edward et al. 2018. “Identifying High-Priority Proteins Across the Human Diseasome Using Semantic Similarity.” Journal of Proteome Research. Cite
Kopylov, Arthur T. et al. 2019. “200+ Protein Concentrations in Healthy Human Blood Plasma: Targeted Quantitative SRM SIS Screening of Chromosomes 18, 13, Y, and the Mitochondrial Chromosome Encoded Proteome.” Journal of Proteome Research 18(1): 120–29. Cite