A novel, “Ion Accounting” algorithm has been developed for protein identification using time-resolved, LC-MSE data from 1D and 2D LC-MS experiments. The data from a 1D LC-MS analysis generate a series of precursor-product tables that are initially queried against a protein database using the “Ion Accounting” algorithm. Hereby each precursor and product is associated with only single peptide identification. The database search is a hierarchal process containing three modules. With the first module, the data are matched to only correctly cleaved proteolytic peptides whose precursor and product ion mass tolerances are within 10 and 20 ppm, respectively. With the second module, precursor and product ions that have not yet been assigned are queried against a subset database of the identified proteins from the first module. The second module includes missed cleavages, in-source fragments, neutral losses, and variable modifications. With the last module, the remaining unidentified ions are considered against the complete database for additional protein identifications (including PMF) with improved selectivity and specificity from the elimination of those precursor and product ions from the first two modules.The data from a 2D LC-MS separation of proteolytic peptides is conducted by fractionating the peptides in a first dimension and subsequent separation in a second dimension during the LC-MSE analysis. Each fraction produces a series of precursor-product tables. From these tables, the peptides (precursor-products) that were not distributed over multiple fractions are saved to a “Combined Precursor-Product Table” (CPPT). The peptides that are split among neighboring fractions are combined by precursor mass, precursor retention time, and product ion pattern, and are appended to the CCPT. The final CCPT is submitted to the “Ion Accounting” protein database search engine in a similar fashion to the 1D LC-MS data analysis.
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机译:开发了一种新颖的“离子核算”算法,该算法使用来自一维和二维LC-MS实验的时间分辨的LC-MS E sup>数据进行蛋白质鉴定。一维LC-MS分析得出的数据会生成一系列前体产物表,这些表最初会使用“离子核算”算法针对蛋白质数据库进行查询。因此,每种前体和产物仅与单个肽鉴定相关。数据库搜索是一个包含三个模块的分层过程。使用第一个模块,数据仅与前体和产物离子质量容差分别在10和20 ppm之内的正确裂解的蛋白水解肽相匹配。使用第二个模块,可以根据第一个模块中已识别蛋白质的子集数据库查询尚未分配的前体离子和产物离子。第二个模块包括错过的裂解,源内片段,中性损失和可变修饰。在最后一个模块中,将剩余的未鉴定离子与完整数据库一起考虑以进行额外的蛋白质鉴定(包括PMF),从而消除了前两个模块中的前体离子和产物离子,从而提高了选择性和特异性.2D LC-通过在LC-MS E sup>分析过程中将肽在第一维中分级分离,然后在第二维中分离,进行蛋白水解肽的MS分离。每个部分都会生成一系列前体-产品表。从这些表中,未分布在多个馏分中的肽(前体产物)被保存到“组合前体产物表”(CPPT)中。通过前体质量,前体保留时间和产物离子图谱将在相邻馏分之间拆分的肽合并在一起,并附加到CCPT上。最终的CCPT以与一维LC-MS数据分析类似的方式提交给“离子核算”蛋白质数据库搜索引擎。
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