Department of Industrial Engineering, University of Washington, Seattle, Washington 98195, USA.
J Proteome Res. 2010 Jun 4;9(6):3270-9. doi: 10.1021/pr100205k.
Shotgun proteomics separates peptides by chromatography and precursor mass over charge, yet in almost any large data set of a complex sample, there will be some tandem mass spectra containing more than one peptide. These mixture spectra contain two coeluting peptides with close precursor mass over charge, and sometimes contain exact isomers, often the same peptide with the same modification in two different positions. Isomers present a problem when the position of the modification is of special interest, as in histone modification studies or "oxidative footprinting" studies of protein structure. Here we give algorithms for identifying isomeric mixtures, and present results on two different histones and four oxidative footprinting targets. Five of the six targets contain at least one peptide that appears in isomeric mixtures, but in none of the cases are mixtures so prevalent that they greatly impact the overall identification rate.
shotgun 蛋白质组学通过色谱和前体质量与电荷比分离肽，但在几乎任何复杂样本的大型数据集，都会有一些串联质谱包含多个肽。这些混合谱包含两个具有相近前体质量与电荷比的共洗脱肽，有时还包含精确的异构体，通常是同一肽在两个不同位置具有相同的修饰。当修饰的位置特别重要时，异构体就会成为一个问题，例如在组蛋白修饰研究或蛋白质结构的“氧化足迹”研究中。这里我们给出了识别异构体混合物的算法，并给出了两种不同的组蛋白和四种氧化足迹靶标的结果。六个靶标中有五个至少含有一个出现在异构体混合物中的肽，但在任何情况下，混合物都没有那么普遍，以至于它们极大地影响了整体鉴定率。
