Title: Advanced Proteomics and Metabolomics Studies of Type 2 Diabetes and Pre-Diabetes
EMSL Project ID
16303a
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
2008-09-30
End Date
2011-10-03
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
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
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, 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.