Department of Chemical Engineering, Princeton University, Princeton, New Jersey 08544-5263, USA.
Mol Cell Proteomics. 2009 Nov;8(11):2527-43. doi: 10.1074/mcp.M900144-MCP200. Epub 2009 Aug 7.
Here we present a novel methodology for the identification of the targeted post-translational modifications present in highly modified proteins using mixed integer linear optimization and electron transfer dissociation (ETD) tandem mass spectrometry. For a given ETD tandem mass spectrum, the rigorous set of modified forms that satisfy the mass of the precursor ion, within some tolerance error, are enumerated by solving a feasibility problem via mixed integer linear optimization. The enumeration of the entire superset of modified forms enables the method to normalize the relative contributions of the individual modification sites. Given the entire set of modified forms, a superposition problem is then formulated using mixed integer linear optimization to determine the relative fractions of the modified forms that are present in the multiplexed ETD tandem mass spectrum. Chromatographic information in the mass and time dimension is utilized to assess the likelihood of the assigned modification states, to average several tandem mass spectra for confident identification of lower level forms, and to infer modification states of partially assigned spectra. The utility of the proposed computational framework is demonstrated on an entire LC-MS/MS ETD experiment corresponding to a mixture of highly modified histone peptides. This new computational method will facilitate the unprecedented LC-MS/MS ETD analysis of many hypermodified proteins and offer novel biological insight into these previously understudied systems.
我们提出了一种新的方法,用于使用混合整数线性优化和电子转移解离(ETD)串联质谱鉴定高度修饰蛋白中存在的靶向翻译后修饰。对于给定的 ETD 串联质谱,通过混合整数线性优化解决可行性问题,可以枚举满足前体离子质量的严格的修饰形式集,在一定的容忍误差范围内。修饰形式的整个超集的枚举使得该方法能够归一化各个修饰位点的相对贡献。给定整个修饰形式集,然后使用混合整数线性优化来制定叠加问题,以确定在多路 ETD 串联质谱中存在的修饰形式的相对分数。在质量和时间维度上的色谱信息用于评估所分配的修饰状态的可能性,对几个串联质谱进行平均以进行置信度识别,以及推断部分分配的光谱的修饰状态。在所提出的计算框架的实用性在对应于高度修饰组蛋白肽混合物的整个 LC-MS/MS ETD 实验上进行了证明。这种新的计算方法将促进对许多超修饰蛋白的前所未有的 LC-MS/MS ETD 分析,并为这些以前研究不足的系统提供新的生物学见解。