University of Minnesota
University of Minnesota
College of Biological Sciences

Timothy J Griffin

Ph.D., University of Wisconsin, 1999
Associate Professor, BMBB; Director, Center for Mass Spectrometry and Proteomics
Telephone: (612) 624-5249 Fax: (612) 624-0432
Director, Center for Mass Spectrometry and Proteomics Ph.D., University of Wisconsin, 1999 Postdoctoral Research, University of Washington and Institute for Systems Biology, 1999-2003

Office: 7-134 MCB

Laboratory: 7-166 MCB
Telephone: (612) 624-0381

Research Group

Publication List

Recent news from the Griffin lab

  • Grant funding:  An NSF grant (Griffin, PI) was recently funded to develop the Galaxy bioinformatics framework for mass spectrometry-based proteomics software applications.  A summary of the grant can be found here
  • A recent paper demonstrated the benefits of online nano Electrostatic Repulsion-Hydrophilic Interaction Chromatography (ERLIC) for shotgun proteomics
  • Another recent paper used a novel approach to profile the metaproteome of human saliva, providing the most comprehensive map of proteins in this fluid derived from microbial organisms

Research Description

Work in our group involves 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. These tools must be capable of measuring the many properties of proteins that collectively determine their function. These properties include protein abundance, sub-cellular localization, post-translational modifications, associations in non-covalent complexes and biochemical activity. Mass spectrometry provides a highly powerful tool that can aid in measuring these various protein properties, in a high-throughput manner. The development and application of these tools is highly interdisciplinary in nature, integrating front-end molecular biology and biochemical methods, protein and peptide chemistry, analytical separations, instrumental analysis, and back-end computation and bioinformatics for data analysis and biological interpretation.

Photograph of Dr. Griffin's research

Ongoing research projects in the laboratory include:

• Studies of oral cancer progression and the salivary proteome using a variety of quantitative proteomic strategies, in collaboration with researchers from the Dental School, Medical School, Computer Science and Biostatistics at the University of Minnesota

• Studies of protein post-translational, as well as under-appreciated oxidative stress-induced reactive carbonyl modifications to amino acid side chains

• Numerous collaborative research projects. For example, we study the biochemistry of the nutrient regulator mTOR via collaboration with Dr. Do-Hyung Kim, Associate Professor, BMBB

We also work closely with the Center for Mass Spectrometry and Proteomics (CMSP) and the Minnesota Supercomputing Institute (MSI) at the University of Minnesota.

Recent Publications

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)

Bandhakavi, S. and Griffin, T.J. (2011) Dynamic range compression: a solution for proteomic biomarker discovery? Bioanalysis, 3: 2053-6. PMID: 21942515

Bandhakavi. S., Markowski, T.W., Xie, H. and Griffin, T.J. (2011) Three dimensional peptide fractionation for highly sensitive nanoscale LC-based shotgun proteomic analysis of complex protein mixtures, Methods Mol Biol, 790: 47-56.  PMID: 21948405

de Jong, E. P., Koopmeiners, J. S.,  and Griffin, T. J.  (2011)  Sample collection and handling considerations for peptidomic studies in whole saliva; implications for biomarker discovery.  Clin Chem Acta.  412: 2284-8.  PMID: 21889499 (PMCID in process)

Kooren, JA, Rhodus, NL, Tang, C, Jagtap, PD, Horrigan, BJ, Griffin, TJ (2011) Evaluating the potential of a novel oral lesion exudate collection method coupled with mass spectrometry-based proteomics for oral cancer biomarker discovery.  Clin Proteomics, 8: 13. PMID: 21914210 (PMCID in process)

Stone MD, Chen X, McGowan T, Bandhakavi S, Cheng B, Rhodus NL, Griffin T.J. (2011) Large-Scale Phosphoproteomics Analysis of Whole Saliva Reveals a Distinct Phosphorylation Pattern. J Proteome Res. 10, 1728-36. PMID: 21299198 (PMCID in process)

Bandhakavi, S., Van Riper, S.K., Tawfik, P.N., Stone, M.D., Haddad, T., Rhodus, N.L., Carlis, J.V., Griffin, T.J. (2011) Hexapeptide Libraries for Enhanced Protein PTM Identification and Relative Abundance Profiling in Whole Human Saliva.  J Proteome Res., 10, 1052-61. PMID: 21142092 (PMCID in process)

Stone, M.D., Odland, R.M., McGowan, T., Onsongo, G., Tang, C., Rhodus, N.L., Jagtap, P., Bandhakavi, S. and Griffin, T.J.(2010) Novel In Situ Collection of Tumor Interstitial Fluid from a Head and Neck Squamous Carcinoma Reveals a Unique Proteome with Diagnostic Potential, Clin Proteomics, 6, 75-82. PMID: 20930922

Onsongo, G., Stone, M.D., Van Riper, S.D., Chilton, J., Wu, B., Higgins, L., Lund, T.C., Carlis, J.V. and Griffin, T.J. (2010) LTQ-iQuant:  A freely-available software pipeline for automated and accurate protein quantification of isobaric tagged peptide data from LTQ instruments, Proteomics, 10, 3533-8. PMID: 20821086

de Jong, E.P., Xie, H., Onsongo, G., Stone, M.D., Chen, X., Kooren, J.A., Refsland, E.W., Griffin, R.J., Ondrey, F.G., Wu, B., Le, C.T., Rhodus, N.L., Carlis, J.V. and Griffin, T.J. (2010) Quantitative proteomics reveals myosin and actin as promising saliva biomarkers for distinguishing pre-malignant and malignant oral lesions, PloS ONE, 5, e11148.PMID: 20567502

Roe, M.R., McGowan, T.F., Thompson, L.V. and Griffin, T.J. (2010) Targeted 18O-labeling for improved proteomic analysis of carbonylated peptides by mass spectrometry, J Am Soc Mass Spectrom, 21, 1190–1203.  PMID: 20434358

Rudney, J.D, Xie, H., Rhodus, N.L., Ondrey, F.G. and Griffin, T.J. (2010) A metaproteomic analysis of the human salivary microbiota by three-dimensional peptide fractionation and tandem mass spectrometry.  Molecular Oral Microbiology, 25, 38-49. PMID: 20331792

Bandhakavi S., Kim Y.M., Ro S.H., Xie H., Onsongo G., Jun C.B., Kim D.H., and Griffin T.J. (2010) Quantitative nuclear proteomics identifies mTOR regulation of DNA damage response. Mol Cellular Proteomics, 9, 403-14.  PMID: 19955088