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Timothy J Griffin

Professor; Director, Center for Mass Spectrometry and Proteomics


Research Description

Work in my group focuses on the development and application of mass spectrometry-based tools to study proteins and proteomes. The goal of this work is to provide the necessary tools to enable the system-wide characterization of proteins expressed within a cell, tissue, biological fluid or organism, in order to better understand basic mechanisms of biological function and disease. My group also works on the Galaxy for proteomics, or Galaxy-P project, which focuses on “multi-omic” analysis integrating genomic, proteomic and metabolomic data to gain new insights into biological systems.  Our work is highly interdisciplinary and collaborative, working across the fields of analytical chemistry, computer science and biochemistry.  We work with numerous researchers to apply our tools and technologies to problems of biological and biomedical importance.

For more information on the Galaxy-P project and research team go to:


Selected Recent Publications

Gulcev M, Reilly C, Griffin TJ, Broeckling CD, Sandri BJ, Witthuhn BA, Hodgson SW, Woodruff PG, Wendt CH. Tryptophan catabolism in acute exacerbations of chronic obstructive pulmonary disease. (2016) Int J Chron Obstruct Pulmon Dis. 11:2435-2446. PMID: 27729784

Thu YM, Van Riper SK, Higgins L, Zhang T, Becker JR, Markowski TW, Nguyen HD, Griffin TJ, Bielinsky AK. (2016) Slx5/Slx8 Promotes Replication Stress Tolerance by Facilitating Mitotic Progression.  Cell Rep. 15:1254-65. PMID: 27134171

Anderson KJ, Vermillion KL, Jagtap P, Johnson JE, Griffin TJ, Andrews MT. (2016) Proteogenomic Analysis of a Hibernating Mammal Indicates Contribution of Skeletal Muscle Physiology to the Hibernation Phenotype.  J Proteome Res. 15:1253-61 PMID: 26903422

Van Riper, S.K., Higgins, L., Carlis, J.V. and Griffin, T.J.  (2016) RIPPER: a framework for MS1 only metabolomics and proteomics label-free relative quantification, Bioinformatics,32:2035-7 PMID: 27153682

Rudney, J.D., Jagtap, P.D., Reilly, C.S., Chen, R., Markowski, T.S., Higgins, L., Johnson, J.E., and Griffin T.J.  (2015) Protein relative abundance patterns associated with sucrose-induced dysbiosis are conserved across taxonomically diverse oral microcosm biofilm models of dental caries, Microbiome, 3: 69. PMID: 26684897

Boekel,J., Chilton, J.M., Cooke, I.R., Horvatovich, P.L., Jagtap P.D, Käll, L., Lehtiö, J., Lukasse, P., Moerland, P.D. and Griffin, T.J. (2015)  Multi-omic data analysis using Galaxy, Nature Biotechnology, 33: 137–139 PMID: 25658277

Jagtap PD, Johnson JE, Onsongo G, Sadler FW, Murray K, Wang Y, Sheynkman GM, Bandhakavi S, Smith LM, Griffin TJ. (2014)  Flexible and accessible workflows for improved proteogenomic analysis using the Galaxy framework. J Proteome Res, 13: 5898-908 PMID: 25301683 PMCID: PMC4261978

Sheynkman GM, Johnson JE, Jagtap PD, Shortreed MR, Onsongo G, Frey BL, Griffin TJ, Smith LM. (2014) Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations, BMC Genomics 15: 703. PMID: 25149441; PMCID: PMC4158061

Yang, Y., Rhodus, N.L., Ondrey, F.G., Wuertz, B.R.K., Chen, X., Zhu, Y., and Griffin, T.J.  (2014)  Quantitative proteomic analysis of oral brush biopsies identifies secretory leukocyte protease inhibitor as a promising, mechanism-based oral cancer biomarker PLoSONE, 9, e95389. PMID: 24748380; PMCID: PMC3991667

Van Riper, S.K., de Jong, E.P., Higgins, L., Carlis, J.V. and Griffin, T.J. (2014)  Improved intensity-based label free quantification via proximity-based intensity normalization (PIN) J Proteome Res, 13:1281-92.  PMID: 22950739 PMCID; PMCID: PMC3487405

Jagtap P., Goslinga J., Kooren J.A., McGowan T., Wroblewski M.S., Seymour S.L., Griffin T.J. (2013) A two-step database search method improves sensitivity in peptide sequence matches for metaproteomics and proteogenomics studies.  Proteomics, 13: 1352-7. PMID: 23412978; PMCID: PMC3633484

Jagtap, P., McGowan, T.,  Bandhakavi, S., Tu, Z. J., Seymour, S., Griffin, T.J. and Rudney, J.D. (2012) Deep metaproteomic analysis of human salivary supernatant. Proteomics 12: 992-1001. PMID: 22522805; PMCID: PMC3517020

de Jong E, Griffin T.J.  (2012) Online nanoscale ERLIC-MS outperforms RPLC-MS for shotgun proteomics in complex mixtures. J Proteome Res, 11, 5059-64. PMID: 22950739; PMCID: PMC3487405

Kim, Y.M., Stone, M., Hwang, T.H., Kim, Y.G., Dunlevy, J.R., Griffin, T.J. and Kim, D.H. (2012) SH3BP4 is a negative regulator of amino acid-Rag GTPase-mTORC1 signaling. Molecular Cell 46. (PDF)


(612) 624-5249 Fax: (612) 624-0432

7-144 MCB
420 Washington Ave SE
Minneapolis, MN 55455