Identification of Proteomic Profiles and Biomarkers in Complex Microbial Systems absent of Genomic Sequence Data
This project will identify protein profiles and biomarkers in an ecosystem or community using proteomic analysis where the genomes of constituent organisms have not been, or cannot be, sequenced, thus overcoming limitations around annotation requirements of many proteomics methods.
This project will develop a methodology for discovering protein profiles and biomarkers in the absence of genome-specific annotations..Proteomic fingerprinting will analyze samples by LC-MS-MS for which a genome sequence is unlikely to exist. The goal of this project is to characterize, or fingerprint, the state of a non-annotated microbial community using LC-MS summary profiles (presence/absence, elution time, mass, abundance…) of non-specific peptide aliases (i.e., genome-free MassTags), and then compare community proteomic fingerprints across community states. This project will produce 3 or more sets of results for each experiment sample. These results include a set of annotated lists of observed MassTags featuring one list for each LC-MS injection; a LC-MS injection pedigree file summarizing the experiment and processing history of each injection; and a summary set of annotated lists of MassTags featuring one list for each set of replicate LC-MS injections – these are the proteomic fingerprints. Other results will include tabular and graphical summaries of comparisons across community states.
The proteomic profiling will be validated on samples of limited complexity with known genomes. The proteomic profiling methodology will then be used to characterize changes in the protein profiles of a biofilm community under controlled uranium stress and finally applied to a hyporheic zone microbial community before and after a controlled stress. Success will provide a mechanism to evaluate ecosystem protein profile changes without genomic sequence information for community constituents.
Point of Contact: Scott Baker