Xiao Kaijie, Yu Fan, Fang Houqin, Xue Bingbing, Liu Yan, Tian Zhixin
Department of Chemistry and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai 200092, China.
Sci Rep. 2015 Oct 6;5:14755. doi: 10.1038/srep14755.
It has long been an analytical challenge to accurately and efficiently resolve extremely dense overlapping isotopic envelopes (OIEs) in protein tandem mass spectra to confidently identify proteins. Here, we report a computationally efficient method, called OIE_CARE, to resolve OIEs by calculating the relative deviation between the ideal and observed experimental abundance. In the OIE_CARE method, the ideal experimental abundance of a particular overlapping isotopic peak (OIP) is first calculated for all the OIEs sharing this OIP. The relative deviation (RD) of the overall observed experimental abundance of this OIP relative to the summed ideal value is then calculated. The final individual abundance of the OIP for each OIE is the individual ideal experimental abundance multiplied by 1 + RD. Initial studies were performed using higher-energy collisional dissociation tandem mass spectra on myoglobin (with direct infusion) and the intact E. coli proteome (with liquid chromatographic separation). Comprehensive data at the protein and proteome levels, high confidence and good reproducibility were achieved. The resolving method reported here can, in principle, be extended to resolve any envelope-type overlapping data for which the corresponding theoretical reference values are available.
长期以来，在蛋白质串联质谱中准确、高效地解析极其密集的重叠同位素包络（OIEs）以可靠地鉴定蛋白质一直是一项分析挑战。在此，我们报告一种计算效率高的方法，称为OIE_CARE，通过计算理想丰度与观察到的实验丰度之间的相对偏差来解析OIEs。在OIE_CARE方法中，首先针对共享该特定重叠同位素峰（OIP）的所有OIEs计算该OIP的理想实验丰度。然后计算该OIP的总体观察实验丰度相对于理想值总和的相对偏差（RD）。每个OIE的OIP的最终个体丰度是个体理想实验丰度乘以1 + RD。最初的研究使用了对肌红蛋白（直接进样）和完整大肠杆菌蛋白质组（液相色谱分离）的高能碰撞解离串联质谱。在蛋白质和蛋白质组水平上获得了全面的数据、高可信度和良好的重现性。本文报道的解析方法原则上可扩展用于解析任何具有相应理论参考值的包络型重叠数据。
