Department of Molecular Systems Biology, University of Vienna, Faculty of Life Sciences, Althanstrasse 14, A-1090, Vienna, Austria.
J Proteome Res. 2011 Jul 1;10(7):2979-91. doi: 10.1021/pr101109a. Epub 2011 May 26.
Mass Accuracy Precursor Alignment is a fast and flexible method for comparative proteome analysis that allows the comparison of unprecedented numbers of shotgun proteomics analyses on a personal computer in a matter of hours. We compared 183 LC-MS analyses and more than 2 million MS/MS spectra and could define and separate the proteomic phenotypes of field grown tubers of 12 tetraploid cultivars of the crop plant Solanum tuberosum. Protein isoforms of patatin as well as other major gene families such as lipoxygenase and cysteine protease inhibitor that regulate tuber development were found to be the primary source of variability between the cultivars. This suggests that differentially expressed protein isoforms modulate genotype specific tuber development and the plant phenotype. We properly assigned the measured abundance of tryptic peptides to different protein isoforms that share extensive stretches of primary structure and thus inferred their abundance. Peptides unique to different protein isoforms were used to classify the remaining peptides assigned to the entire subset of isoforms based on a common abundance profile using multivariate statistical procedures. We identified nearly 4000 proteins which we used for quantitative functional annotation making this the most extensive study of the tuber proteome to date.
质量精度前体对齐是一种快速灵活的比较蛋白质组学分析方法，允许在个人计算机上对前所未有的数量的鸟枪法蛋白质组学分析进行比较，只需要几个小时。我们比较了 183 个 LC-MS 分析和 200 多万个 MS/MS 谱，可以定义和分离 12 个四倍体栽培种马铃薯田间生长块茎的蛋白质组表型。发现马铃薯蛋白同工型以及调节块茎发育的其他主要基因家族（如脂氧合酶和半胱氨酸蛋白酶抑制剂）是品种间变异的主要来源。这表明差异表达的蛋白质同工型调节特定于基因型的块茎发育和植物表型。我们正确地将测得的胰蛋白酶肽的丰度分配到不同的蛋白质同工型上，这些同工型共享广泛的一级结构，从而推断它们的丰度。不同蛋白质同工型特有的肽用于根据共同的丰度分布使用多元统计程序对分配给整个同工型子集的剩余肽进行分类。我们鉴定了近 4000 种蛋白质，我们用于定量功能注释，这是迄今为止对块茎蛋白质组进行的最广泛的研究。
