Assistant Professor

Biology Department
Chemistry and Biological Chemistry Department

Education and Training

B.S. Cornell University
Chemistry

Ph.D. University of Virginia
Analytical Biochemistry

Contact

E-mail: plattm@rpi.edu
Phone: (518) 276-3273
Fax: (518) 276-4887

Office: Cogswell Laboratory Rm. 133
Lab: Cogswell Laboratory Rm. 130

Rensselaer Polytechnic Institute
110 8th Street,
Troy, NY 12180

Research Interests

Proteomics, Protein Phosphorylation, Mass Spectrometry, Bioinformatics

The research in our laboratory involves the use of mass spectrometry to identify proteins within biological systems. Specifically, we are focused on the global identification of protein phosphorylation sites and on the determination of differential protein expression. We are also developing novel chemical and bioinformatic approaches in order to extend the field of proteomics into other research areas and to allow proteomic methodologies to be applied to a wider array of sample types.

Global Identification of Specific Sites of Protein Phosphorylation. Protein phosphorylation is a post-translational modification that is known to play a role in diverse processes such as cell cycle progression, signal transduction, and DNA repair. However, understanding the manner in which phosphorylation regulates protein structure and function requires that the exact sites of modification be determined. In our laboratory, we utilize custom-made immobilized metal affinity chromatography (IMAC) microcapillary columns for the selective enrichment of phosphopeptides from complex protein digests. Identification of the exact amino acid to which the phosphate moiety is attached is accomplished using tandem mass spectrometry (MS/MS), an analytical technique which allows for the rapid sequencing of low abundance peptides. In addition, we have adopted electron transfer dissociation (ETD) as a novel method for the fragmentation of phosphopeptides, as this approach provides better sequence coverage and more readily interpretable MS/MS spectra than the more conventional collisionally-activated dissociation (CID) method. Current collaborative projects in the laboratory involve the identification of phosphorylation changes initiated during mammalian sperm capacitation and the determination of the dynamic interplay between phosphorylation and other post-translational modifications (PTMs) on the protein tubulin.

Comprehensive Determination of Differential Protein Expression. One of the major objectives of protein biochemistry is the comprehensive elucidation of protein expression in dissimilar cell types or in cells grown under different environmental conditions. Although attempts have been made to measure relative protein expression indirectly through the microarray analysis of mRNA, this approach is limited by the fact that gene transcription does not always correlate with protein expression. In our laboratory, we use either metabolic (e.g. stable isotope labeling with amino acids in cell culture (SILAC)) or chemical means to directly tag different protein/peptide populations with an isotopic label. Samples are mixed and, in order to address sample complexity, loaded onto an in-house constructed microcapillary high-pressure liquid chromatography (µHPLC) column. Chemical species are then gradient-eluted directly into the mass spectrometer. The instrument speed, dynamic range, and MS/MS capability permits comprehensive peptide/protein sequencing, while the isotopic labeling allows for the relative quantitation of protein expression between sample populations. Current collaborative projects in the laboratory involve the identification of specific nuclear proteins responsible for high-producing Chinese hamster ovary (CHO) cell lines and the determination of differential protein expression in bacteria grown under nitrogen starvation conditions.

Selected Publications

Mark D. Platt, Ana Maria Salicioni, Donald F. Hunt, and Pablo E. Visconti; “Use of Differential Isotopic Labeling and Mass Spectrometry to Analyze Capacitation-Associated Changes in the Phosphorylation Status of Mouse Sperm Proteins” Journal of Proteome Research, 2009; 8(3): 1431-1440.

Mark D. Platt, Sung-Hei Hwang, Michael J. Schurr, Jill Schurr, Roger C. Levesque, Ahmet C. Karubulut, Sang Sun Yoon, Patrick A. Limbach, John J. Rowe, Gee W.Lau, Donald F. Hunt and Daniel J. Hassett; “Proteogenomic Analysis of Pseudomonas aeruginosa Grown During Anaerobic Nitrate and Nitrite Respiration” Journal of Bacteriology, 2008; 190(8): 2739-2758.

C. Huie Lin, Mark D. Platt, Scott B. Ficarro, Mark H. Hoofnagle, Jeffrey Shabanowitz, Donald F. Hunt, Lucio Comai, and Gary K. Owens; “Mass Spectrometric Identification of Phosphorylation Sites of the rRNA Transcription Factor Upstream Binding Factor (UBF)” American Journal of Physiology: Cell Physiology, 2007; 292(5): C1617-1624.

Benjamin A. Garcia, Mark D. Platt, Timothy L. Born, Jeffrey Shabanowitz, Norman A. Marcus, and Donald F. Hunt; “Protein Profile of Osteoarthritic Human Articular Cartilage Using Tandem Mass Spectrometry” Rapid Communications in Mass Spectrometry, 2006; 20(20): 2999-3006.

Rebecca W. Corbin, Oleg Paliy, Feng Yang, Jeffrey Shabanowitz, Mark D. Platt, Charles E. Lyons, Jr., Karen Root, Jon McAuliffe, Michael I. Jordan, Sydney Kustu, Eric Soupene, and Donald F. Hunt; “Toward a protein profile of Escherichia coli: Comparison to its transcription profile” Proceedings of the National Academy of Sciences of the United States of America, 2003; 100: 9232-9237.

Daniel J. Hassett, Patrick A. Limbach, Robert F. Hennigan, Karl E. Klose, Robert E. W. Hancock, Mark D. Platt, and Donald F. Hunt; “Bacterial biofilms of importance to medicine and bioterrorism: proteomic techniques to identify novel vaccine components and drug targets” Expert Opinion on Biological Therapy, 2003; 3(8): 1201-1207.