SUBPROJECT 2
The characterization of the proteome dataset of a complex natural microbial community will require a systematic experimental plan to push the capabilities of current mass spectrometry techniques as well as develop the next generation of technology. Our preliminary proteomic data on an AMD biofilm demonstrated tremendous potential for defining the activity wihtin a natural microbial community. We will evaluate and demonstrate high performance MS technology for deeper and more comprehensive characterization and quantification of the proteins and protein complexes so as to unravel the details of how these ecosystems develop and function. The experimental and computational technologies resulting from this project will help pave the way for the characterization of more complex microbial communities. Imporant aims of our work are to unravel the details of microbial strain variant diversity with high mass accuracy and MS3 experiments and to develop methods for quantification of protein abundance in natural microbial communities to elucidate the major investments of cellular resources.