Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.
J Proteomics. 2011 Aug 12;74(8):1190-200. doi: 10.1016/j.jprot.2011.04.008. Epub 2011 Apr 22.
It is an established fact that allelic variation and post-translational modifications create different variants of proteins, which are observed as isoelectric and size subspecies in two-dimensional gel based proteomics. Here we explore the stromal proteome of spinach and Arabidopsis chloroplast and show that clustering of mass spectra is a useful tool for investigating such variants and detecting modified peptides with amino acid substitutions or post-translational modifications. This study employs data mining by hierarchical clustering of MALDI-MS spectra, using the web version of the SPECLUST program (http://bioinfo.thep.lu.se/speclust.html). The tool can also be used to remove peaks of contaminating proteins and to improve protein identification, especially for species without a fully sequenced genome. Mutually exclusive peptide peaks within a cluster provide a good starting point for MS/MS investigation of modified peptides, here exemplified by the identification of an A to E substitution that accounts for the isoelectric heterogeneity in protein isoforms.
事实上，等位基因变异和翻译后修饰会产生不同的蛋白质变体，这些变体在二维凝胶蛋白质组学中表现为等电点和大小亚种。在这里，我们探索了菠菜和拟南芥叶绿体的基质蛋白质组，并表明质谱聚类是研究这些变体和检测具有氨基酸取代或翻译后修饰的修饰肽的有用工具。本研究通过使用 SPECLUST 程序的网络版本（http://bioinfo.thep.lu.se/speclust.html）对 MALDI-MS 光谱进行层次聚类来进行数据分析挖掘。该工具还可用于去除污染蛋白的峰，提高蛋白鉴定的准确性，尤其是针对那些尚未完成全基因组测序的物种。簇内相互排斥的肽峰为修饰肽的 MS/MS 研究提供了一个良好的起点，这里通过鉴定一个 A 到 E 的取代来举例说明，该取代解释了蛋白质同工型的等电点异质性。
