CEPCEB Members

Songqin Pan Academic Coordinator (Proteomics) Center of Plant Cell Biology Department of Botany and Plant Sciences Noel T. Keen Hall, Room 119 University of California Riverside, CA 92521 Phone: (951) 827-7114 Fax: (951) 827-4437
Background Current Research Interests Selected Publications (Bibliography page)

Background

I received my M.S. in Horticulture from the University of Wisconsin at Madison in 1993 and Ph.D. in Plant Molecular and Cellular Biology from the University of Florida at Gainesville in 1998. For my doctoral research, I studied basic mechanisms in transcriptional regulation in higher plants, under the direction of Dr. William B. Gurley. The research was focused on the characterization of the general transcription factors such as the TATA-box binding protein (TBP), transcription factor II B (TFIIB), the TBP-associated factors (TAFs), as well as other transcriptional regulators such as 14-3-3, VP16, Gal4, ftzQ, and GBF. The functional roles of the protein-protein interactions between these factors and their interactions with promoter elements in both basal and activated transcription in plant cells were of particular interest in my projects.

In early 2001, I joined the Los Alamos National Laboratory as a Postdoc Research Associate to work with Dr. Xian Chen who is a recipient of the Presidential Early Career Award for Scientists and Engineers. My research was to develop biological mass spectrometry methods that can be used in the studies of the complex human proteome. These methods employed amino acids coded mass-tagging (AACM) strategy to facilitate accurate protein identification and quantification in the context of a biological process.

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With combined experience in both plant cell biology and biological mass spectrometry, I would like to pursue research interests in the area of plant proteomics for my current position as an Academic Coordinator in Proteomics. I will develop methods that can mass-tag plant proteomes using the stable isotope labeled amino acid precursors. A mass-tagged amino acid residue can serve as an internal mass signature in an MS spectrum to track amino acid compositions of the tryptic peptides as shown in Fig. 1. This so-called amino acids coded mass-tagging (AACM) approach can significantly increase specificity and accuracy of protein identification in database search and reduce both false-positive and false-negative results. Furthermore, the MS isotopic ratios between unlabeled and labeled peptides can be used as a quantitative method to accurately determine protein levels in differential expression in a biological system (Fig. 2). The usefulness of these methods has been demonstrated in MS-based proteomics in both human and yeast. Combined with the state-of-art mass spectrometry instruments such as Q-TOF, Q-STAR and LC-MALDIprep in our proteomics lab, the AACM approach should be a powerful tool to resolve high mass degeneracy in large complex proteomes of both human and plants.

Figure 1. Mass-tagged peptides in the MALDI-TOF MS showing the characteristic isotope patterns induced by the incorporation of various types of labeled amino acids. The labels are listed at the right; 'K'-lysine, 'L'-leucine, 'M'-methionine, 'S'-serine, 'Y'-tyrosin, and 'U' for the unlabeled control. The isotope pattern induced by each labeled amino acid is marked as "*".

Figure 2. HS response in human cells showing differential protein expressions as determined by the isotopic ratios of labeled lysine in LC-MS. A) induced expression of HSP70. B) induced expression of Vimentin. C) Actin expression not changed.

Selected Publications (Bibliography page)

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