Armengaud Jean
CEA-Marcoule, DRF/JOLIOT/DMTS/SPI/Li2D, Laboratory "Innovative Technologies for Detection and Diagnostics", BP 17171, 30200, Bagnols-sur-Cèze, France.
Methods Mol Biol. 2017;1616:107-120. doi: 10.1007/978-1-4939-7037-7_6.
Whole-cell MALDI-TOF has become a robust and widely used tool to quickly identify any pathogen. In addition to being routinely used in hospitals, it is also useful for low cost dereplication in large scale screening procedures of new environmental isolates for environmental biotechnology or taxonomical applications. Here, I describe how specific biomarkers can be defined using shotgun proteomics and whole-cell MALDI-TOF mass spectrometry. Based on MALDI-TOF spectra recorded on a given set of pathogens with internal calibrants, m/z values of interest are extracted. The proteins which contribute to these peaks are deduced from label-free shotgun proteomics measurements carried out on the same sample. Quantitative information based on the spectral count approach allows ranking the most probable candidates. Proteogenomic approaches help to define whether these proteins give the same m/z values along the whole taxon under consideration or result in heterogeneous lists. These specific biomarkers nicely complement conventional profiling approaches and may help to better define groups of organisms, for example at the subspecies level.
全细胞基质辅助激光解吸电离飞行时间质谱（Whole-cell MALDI-TOF）已成为一种强大且广泛应用的工具，可快速鉴定任何病原体。除了在医院常规使用外，它对于环境生物技术或分类学应用中大规模筛选新环境分离株的低成本重复排除也很有用。在此，我描述了如何使用鸟枪法蛋白质组学和全细胞MALDI-TOF质谱来定义特定的生物标志物。基于使用内部校准物在给定病原体集上记录的MALDI-TOF光谱，提取感兴趣的m/z值。对同一样本进行的无标记鸟枪法蛋白质组学测量可推断出产生这些峰的蛋白质。基于光谱计数方法的定量信息可对最可能的候选物进行排序。蛋白质基因组学方法有助于确定这些蛋白质在整个所考虑的分类单元中是否给出相同的m/z值，或者是否导致异质列表。这些特定的生物标志物很好地补充了传统的分析方法，并可能有助于更好地定义生物体群体，例如在亚种水平。
