Top-Down Identification of Protein Biomarkers in Bacteria with Unsequenced Genomes. Export

@article{citeulike:6077110, abstract = {MALDI mass spectrometry-based systems for rapid characterization of microorganisms in biodefense or medical diagnostics usually detect intact proteins in the 5000−20,000 Da range. To evaluate the reliability of species discrimination, and also for forensic applications, it is important that these biomarker proteins be identified. In the present study we apply high resolution tandem mass analysis on an Orbitrap and top-down bioinformatics to identify major biomarker proteins observed in MALDI spectra of intact bacteria for which little genomic or protein sequence information is available. The strategy depends on recognition of proteins with very high homology in related (sequenced) species, making it possible to place unsequenced organisms in their correct phylogenetic context. We show that this rapid proteomics based approach to phylogenetic characterization produces similar results to the traditional techniques, and may even be applied to target organisms of undetermined taxonomy. We further discuss important issues in combining genomics/proteomics databases and MALDI MS for the rapid characterization of microorganisms.}, author = {Wynne, Colin and Fenselau, Catherine and Demirev, Plamen A. and Edwards, Nathan}, citeulike-article-id = {6077110}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/ac9016677}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/ac9016677}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19883058}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19883058}, day = {2}, doi = {10.1021/ac9016677}, issn = {1520-6882}, journal = {Analytical chemistry}, keywords = {microorganism-identification, phylogenetic-analysis, prosight, protein-identification, proteomics, top-down}, month = {November}, number = {23}, pages = {9633--9642}, posted-at = {2009-11-05 22:20:30}, priority = {2}, title = {Top-Down Identification of Protein Biomarkers in Bacteria with Unsequenced Genomes.}, url = {http://dx.doi.org/10.1021/ac9016677}, volume = {81}, year = {2009} }

TY - JOUR ID - citeulike:6077110 L3 - citeulike-article-id:6077110 N2 - MALDI mass spectrometry-based systems for rapid characterization of microorganisms in biodefense or medical diagnostics usually detect intact proteins in the 5000−20,000 Da range. To evaluate the reliability of species discrimination, and also for forensic applications, it is important that these biomarker proteins be identified. In the present study we apply high resolution tandem mass analysis on an Orbitrap and top-down bioinformatics to identify major biomarker proteins observed in MALDI spectra of intact bacteria for which little genomic or protein sequence information is available. The strategy depends on recognition of proteins with very high homology in related (sequenced) species, making it possible to place unsequenced organisms in their correct phylogenetic context. We show that this rapid proteomics based approach to phylogenetic characterization produces similar results to the traditional techniques, and may even be applied to target organisms of undetermined taxonomy. We further discuss important issues in combining genomics/proteomics databases and MALDI MS for the rapid characterization of microorganisms. IS - 23 JF - Analytical chemistry SN - 1520-6882 EP - 9642 TI - Top-Down Identification of Protein Biomarkers in Bacteria with Unsequenced Genomes. VL - 81 SP - 9633 KW - microorganism-identification KW - phylogenetic-analysis KW - prosight KW - protein-identification KW - proteomics KW - top-down AU - Wynne, Colin AU - Fenselau, Catherine AU - Demirev, Plamen AU - Edwards, Nathan PY - 2009/11/02/ UR - http://dx.doi.org/10.1021/ac9016677 ER -