Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.
Genome Center of Wisconsin, University of Wisconsin , 425G Henry Mall, Room 3420, Madison, Wisconsin 53706, United States.
J Proteome Res. 2017 Nov 3;16(11):4156-4165. doi: 10.1021/acs.jproteome.7b00516.
A proteoform family is a group of related molecular forms of a protein (proteoforms) derived from the same gene. We have previously described a strategy to identify proteoforms and elucidate proteoform families in complex mixtures of intact proteins. The strategy is based upon measurements of two properties for each proteoform: (i) the accurate proteoform intact-mass, measured by liquid chromatography/mass spectrometry (LC-MS), and (ii) the number of lysine residues in each proteoform, determined using an isotopic labeling approach. These measured properties are then compared with those extracted from a catalog of theoretical proteoforms containing protein sequences and localized post-translational modifications (PTMs) for the organism under study. A match between the measured properties and those in the catalog constitutes an identification of the proteoform. In the present study, this strategy is extended by utilizing a global PTM discovery database and is applied to the widely studied model organism Escherichia coli, providing the most comprehensive elucidation of E. coli proteoforms and proteoform families to date.
蛋白形式家族是指从同一基因衍生而来的一组相关的蛋白质分子形式(蛋白形式)。我们之前描述了一种策略,用于在完整蛋白质的复杂混合物中鉴定蛋白形式和阐明蛋白形式家族。该策略基于对每个蛋白形式的两个特性进行测量:(i)通过液相色谱/质谱(LC-MS)测量的准确蛋白形式完整质量,以及(ii)使用同位素标记方法确定的每个蛋白形式中的赖氨酸残基数。然后将这些测量的特性与从包含研究生物体内的蛋白质序列和局部化翻译后修饰(PTM)的理论蛋白形式目录中提取的特性进行比较。测量的特性与目录中的特性相匹配构成了对蛋白形式的鉴定。在本研究中,通过利用全局 PTM 发现数据库扩展了该策略,并将其应用于广泛研究的模式生物大肠杆菌,提供了迄今为止最全面的大肠杆菌蛋白形式和蛋白形式家族的阐明。