Title: Advanced Proteomics and Metabolomics Studies of Type 2 Diabetes and Pre-Diabetes
EMSL Project ID
16303
Abstract
Abstract: In this five year (R21/R33) project we will apply advanced proteomic and metabolomic nanoflow liquid chromatography-Fourier transform ion cyclotron resonance (FTICR) mass spectrometry technologies in the study of both plasma and blood cells from individuals with normal glucose tolerance (NGT), impaired glucose tolerance (IGT), and recently diagnosed type 2 diabetes (T2DM). The overall approach endeavors to advance the study of Type 2 diabetes and pre-diabetes by identifying biomarkers at the level of the proteome and metabolome that are predictive of Type 2 diabetes and pre-diabetes in vivo. Our approach will utilize proteome-wide stable isotope labeling of peptides, as well as quantitative cysteine-peptide enrichment technology (QCET) and N-linked glycopeptide enrichment strategies to obtain broad proteome coverage and enhance quantitation. We will also utilize very low nanoflow LC separations to minimize ionization suppression and eliminate background ions originating from the solvent, thereby improving normalization of metabolite peak intensities and improve quantitation. This approach will be capable of rapidly identifying and measuring expression levels for thousands of peptides or concentrations of metabolites in a single analysis.
Phase 1 of this project will (a) define the sample processing and LC separation conditions necessary for broad proteome and metabolome coverage in human plasma and blood cell samples, (b) perform a pilot study to define specific differences in the plasma proteome and metabolome of 10 individuals each with NGT, IGT, and T2DM, (c) establish accurate mass and time tag databases for both peptides and metabolites detected in plasma and blood cells from individuals with NGT, IGT, and T2DM, and (d) perform a pilot study to deterimine the feasibility of applying the nanoflow FTICR approch in the identification of non-enzymatically glycated plasma proteins. The refinement of this technological approach will provide the basis for high throughput studies of large numbers of samples. The application of this technology in Phase 2 of the project will involve (a) high throughput studies of large numbers of plasma and blood cell samples from individuals with NGT, IGT, and T2DM, (b) validation of proteomic and metabolomic biomarkers of T2DM and pre-diabetes identified in Phase 1, and (c) refinement of the sample processing and data analysis approach used in the identification of non-enzymatically glycated plasma proteins (Phase 1), in order to identify plasma proteins containing advanced glycation and/or advanced lipoxidation end products (AGEs/ALEs).
Project Details
Start Date
2005-08-31
End Date
2008-08-31
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
A Perspective on the Maillard Reaction and the Analysis of Protein Glycation by Mass Spectrometry: Probing the Pathogenesis of Chronic Disease Qibin Zhang, Jennifer M. Ames, Richard D. Smith, John W. Baynes, and Thomas O. Metz J. Proteome Res., Article ASAP • DOI: 10.1021/pr800858h
Ding, J., Sorensen, C.M., Jaitly, N., Jiang, H., Orton, D.J., Monroe, M.E., Moore, R.J., Smith, R.D., and Metz, T.O. 2008. "Application of the accurate mass and time tag approach in studies of the human blood lipidome." J. Chromatogr. B. Analyt. 871(2):243-252
Gonzales RM, Q Zhang, RC Zangar, RD Smith, and TO Metz. 2011. "Development of a Fibrinogen-Specific Sandwich Enzyme-Linked Immunosorbent Assay Microarray Assay for Distinguishing Between Blood Plasma and Serum Samples." Analytical Biochemistry 414(1):99-102. doi:10.1016/j.ab.2011.02.039
Kangas LJ, TO Metz, G Isaac, BT Schrom, B Ginovska-Pangovska, L Wang, L Tan, RR Lewis, and JH Miller. 2012. "In Silico Identification Software (ISIS): A Machine Learning Approach to Tandem Mass Spectral Identification of Lipids." Bioinformatics 28(13):1705-1713. doi:10.1093/bioinformatics/bts194
Matzke MM, JN Brown, MA Gritsenko, TO Metz, JG Pounds, KD Rodland, AK Shukla, RD Smith, KM Waters, JE McDermott, and BJM Webb-Robertson. 2013. "A Comparative Analysis of Computational Approaches to Relative Protein Quantification Using Peptide Peak Intensities in Label-free LC-MS Proteomics Experiments." Proteomics 13(3-4):493-503. doi:10.1002/pmic.201200269
Metz, T.O., Page, J.S., Baker, E.S., Tang, K., Ding, J., Shen, Y.F., and Smith, R.D. High-resolution separations and improved ion production and transmission in metabolomics. Trends Analyt. Chem. (2008), 27:205-214.
Metz, T.O., Qian, W.-J., Jacobs, J.M., Polpitiya, A.D., Gritsenko, M.A., Jiang, H., Clauss, T.R., Zhang, R., Shukla, A.K., Tolmachev, A.V., Camp, D.G. 2nd, Phillips, L.S., and Smith R.D. Application of LC-MS-based proteomics in the discovery of candidate protein biomarkers of impaired glucose tolerance and type 2 diabetes. Diabetes (2008), 57 (Supplement 1): A315.
Schneider S, and MW Zacharias. 2012. "Combining Geometric Pocket Detection and Desolvation Properties to Detect Putative Ligand Binding Sites on Proteins." Journal of Structural Biology 180(3):546-550. doi:10.1016/j.jsb.2012.09.010
Shvartsburg AA, GI Mezengie, N Leveque, RD Smith, and TO Metz. 2011. "Separation and Classification of Lipids Using Differential Ion Mobility Spectrometry." Journal of the American Society for Mass Spectrometry 22(7):1146-1155. doi:10.1007/s13361-011-0114-z
Zhang Q, AA Schepmoes, JW Brock, S Wu, RJ Moore, SO Purvine, J Baynes, RD Smith, and TO Metz. 2008. "Improved Methods for the Enrichment and Analysis of Glycated Peptides ." Analytical Chemistry 80(24):9822-9829. doi:10.1021/ac801704j
Zhang Q, A Frolov, N Tang, R Hoffmann, T vd Goor, TO Metz, and RD Smith. "Application of electron transfer dissociation mass spectrometry in analyses of non-enzymatically glycated peptides." 2007. Rapid Communications in Mass Spectrometry 21:661-666.
Zhang Q, ME Monroe, AA Schepmoes, TRW Clauss, MA Gritsenko, D Meng, VA Petyuk, RD Smith, and TO Metz. 2011. "Comprehensive Identification of Glycated Peptides and Their Glycation Motifs in Plasma and Erythrocytes of Control and Diabetic Subjects." Journal of Proteome Research 10(7):3076-3088.
Zhang Q, N Tang, JWC Brock, HM Mottaz, JM Ames, JW Baynes, RD Smith, and TO Metz. "Enrichment and analysis of nonenzymatically glycated peptides: boronate affinity chromatography coupled with electron-transfer dissociation mass spectrometry." 2007. Journal of Proteome Research 6:2323-2330.
Zhang, Q., Tang, N., Schepmoes, A.A., Phillips, L.S., Smith, R.D., and Metz, T.O. Proteomic profiling of nonenzymatically glycated proteins in human plasma and erythrocyte membranes. J. Proteome Res. (2008), 7:2025-2032.
Zhang, Q, TO Metz, N Tang, JWC Brock, HM Mottaz, and RD Smith. "Enrichment and analysis of non-enzymatically glycated peptides: boronate affinity chromatography coupled with electron transfer dissociation mass spectrometry." Presented at the 55th Annual ASMS Conference on Mass Spectrometry, June 3-7 2007, Indianapolis, IN
Zhang Q, VA Petyuk, AA Schepmoes, DJ Orton, ME Monroe, F Yang, RD Smith, and TO Metz. 2008. "Analysis of Non-Enzymatically Glycated Peptides: Neutral-Loss Triggered MS3 Versus Multi-Stage Activation Tandem Mass Spectrometry." Rapid Communications in Mass Spectrometry 22(19):3027-3034. doi:10.1002/rcm.3703