The proteome of a cell is made up of the set of proteins being expressed by the cell at any one point in time. Proteins are the essential elements of a cell that enable nearly all of its functional capabilities, from providing the architectural elements that give the cell structure, facilitating cellular construction, regulating cellular metabolism and energy production, to cellular communication. The quantification of their synthesis patterns is critical to characterizing the response of an organism to a changing environment. Proteomics is the process of studying the dynamics of the proteome. While some studies have demonstrated much potential in the use of proteomics to improve understanding the response of organisms to potential climate change, few laboratories have ventured deeply into the study of the proteome, especially in the context of environmental stress. This is in large part due to the complexity and cost of the sophisticated analytical instrumentation required to separate, quantify and identify proteins. In addition, relatively few proteomics analyses exist of non-model organisms for which there is limited genomic information, despite the fact that they are often "model" systems in other biological disciplines, e.g., blue mussels (genus: Mytilus) as bio-indicators for pollution stress.
This five day workshop will introduce twelve participants to the methodology involved in a proteomic analysis: from the separation of proteins by their charge (isoelectric point) and their molecular mass by two-dimensional gel electrophoresis and high-pressure liquid chromatography, the quantification of proteins and subsequent statistical analyses, to the identification of proteins through mass spectrometry, including matrix-assisted laser desorption tandem time of flight (MALDI-ToF-ToF) and electrospray ionization quadrupole time-of-flight (ESI Q-ToF) mass spectrometry. Importantly, participants will have the opportunity to analyze their own samples, generate their own data set, and will be exposed to the various tools that facilitate the interpretation of their results. The goal of this workshop is to introduce participants to proteomics methodologies and incubate several new proteomics projects.
The PI has a track record of training a great number of undergraduates, graduate students, and visiting scholars in proteomic techniques, including mass spectrometry. He has collaborated with a number of colleagues to build a community around environmental proteomics, and organized a symposium on the topic at a recent conference. This workshop is a continuation of his effort to build a larger research community around environmental proteomics. Efforts will be made to recruit participants nationally. These efforts include a number of communications specifically directed to recruit participants from underrepresented groups in STEM, and therefore this project aims to broaden participation in these state-of-the-art approaches. Overall, the proposed workshop promises to build the capacity of the community to conduct proteomic analyses and will help initiate a number of new proteomic projects.
Meeting: Workshop on Comparative Proteomics of Environmental and Pollution Stress, Cal Poly; December 10-14, 2012 The objective of the proteomics field is to study the dynamics of the protein complement, the entire set of proteins present in a cell. Changes in the proteome directly indicate functional changes, such as in energy metabolism and cell signaling. Importantly, a number of changes in the proteome are independent of the genome; they are able to respond faster to environmental signals and are at least an order of magnitude more complex and dynamic than the genome. The five-day, national environmental proteomics workshop provided an introduction to proteomics methodologies with an emphasis on the proteomic responses of non-model and model organisms to environmental stressors. Undergraduate and Masters students from the Tomanek laboratory introduced participants to the basic techniques of analyzing the proteome. Participants learned how to homogenize a tissue, precipitate proteins, determine protein concentrations, separate proteins by two-dimensional gel electrophoresis, visualize and analyze protein abundance patterns, conduct the statistical analysis of these patterns, prepare proteins for mass spectrometry through in-gel trypsin digestion, generate peptide and fragment mass fingerprints through tandem mass spectrometry, and identify proteins through bioinformatic searches with a number of data bases. The participants came from across the US, ranging in geography from the University of Hawaii to Boston University. Nine women and five men, including four from underrepresented groups, ranging in academic rank from Masters and PhD students, to professor participated. Nine participants analyzed their own project’s tissue samples during the workshop and obtained 2D gel images and proteins identifications through tandem mass spectrometry. Based on the preliminary data participants obtained at the workshop, at least four of the participants have since obtained funding to further pursue a proteomic analysis of their samples, including a post-doctoral fellowship from the Smithsonian Institute and an NSF grant. This was the first environmental proteomics workshop in the US and the Tomanek lab is planning to offer additional workshops in the future.
