Top-Down Identification of Protein Biomarkers in Bacteria with Unsequenced Genomes
Top-Down Identification of Protein Biomarkers in Bacteria with Unsequenced Genomes
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DOI：
10.1021/ac9016677
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发表时间：
2009-12-01
影响因子：
7.4
通讯作者：
Edwards, Nathan
中科院分区：
文献类型：
--
作者：
Wynne, Colin;Fenselau, Catherine;Edwards, Nathan
用于生物防御或医学诊断中微生物快速表征的基于MALDI质谱的系统通常检测5000- 20，000 Da范围内的完整蛋白质。为了评估物种区分的可靠性，以及法医应用，重要的是鉴定这些生物标志物蛋白。在本研究中，我们应用高分辨率的串联质量分析的Orbitrap和自上而下的生物信息学，以确定主要的生物标志物蛋白质的MALDI光谱中观察到的完整的细菌的基因组或蛋白质序列信息很少。该策略依赖于识别相关（测序）物种中具有非常高同源性的蛋白质，从而可以将未测序的生物体置于正确的系统发育背景中。我们表明，这种快速的蛋白质组学为基础的方法，系统发育特征产生类似的结果，传统的技术，甚至可能适用于目标生物的未确定的分类。我们进一步讨论了结合基因组学/蛋白质组学数据库和MALDI MS快速表征微生物的重要问题。
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.