Harnessing chromatographic information in proteomics: comprehensive coverage of peptide post-translational and chemical modifications

生物分析化学的迅速发展为人类健康、农业、能源和环境研究等现代科学的许多应用领域提供了巨大的利益。液相色谱-质谱（LC-MS）已成为蛋白质组学应用的首选方法，因为它是最强大的蛋白质/肽分析技术。该技术依赖于LC分离和质谱分析较小的肽：蛋白质水解消化的产物。近年来，大多数开发重点都放在系统的ms组件上。同时，许多研究人员已经认识到LC组分能够提供非常有价值的信息，因为它能够计算被分析分子的保留性质。总的来说，这使得LC-MS成为一把“双刃剑”，两种方法的结果都可以用来改善分析输出和方法本身的设计。几个研究小组一直在开发肽保留预测模型。我的实验室一直走在这些发展的前沿：我们的序列特异性保留计算器（SSRCalc）模型已经成为该领域的基准工具，吸引了蛋白质组学/色谱界以及蛋白质组学设备和软件主要供应商的关注。

Rapid developments in bioanalytical chemistry have provided enormous benefits for many applied fields of modern science including human health, agriculture, energy, and environmental studies. Liquid chromatography - mass spectrometry (LC-MS) has become the method of choice for proteomic applications, as it is the most powerful technique for protein/peptide analysis. This technique relies on LC separation and MS analysis of smaller peptides: products of protein proteolytic digestion. Most of the developmental emphasis in recent years has been on the MS-component of the system. At the same time many researchers have recognized the ability of the LC component to provide very valuable information, given the ability to compute the retention properties of analyzed molecules. Overall this makes LC-MS a “double-edged sword”, where the outcomes from both methods can be used to improve the analysis output and design of the methods themselves. Several research teams have been developing peptide retention prediction models. My laboratory has been at the forefront of these developments: our Sequence Specific Retention Calculator (SSRCalc) model has become a benchmark tool in the field, attracting attention both from the proteomic/chromatographic community and from major vendors of proteomics equipment and software. So far, the vast majority of predictive approaches target peptides, which consist of 20 natural, non-modified amino acids. It is known, however, that proteins may carry numerous post-translational modifications, which often control protein functions in complex biological systems. These modifications cannot be predicted based on genomic sequence, which make proteomics a key methodology for their study. These modifications change both molecular weight and hydrophobicity of analysed peptides. While determining the effect of a modification on the MS properties (mass shift) of a peptide is straightforward, predicting the alteration in chromatographic properties is difficult. The focus of the next cycle of my Discovery Grant is to extend the SSRCalc prediction methodology to peptides with post-translational and chemical modifications. This will 1) provide proteomic researchers with new tools to effectively monitor these modifications; 2) help us to develop comprehensive solutions to this fundamental problem in separation chemistry while also gaining new insights into underlying chemical and biological processes; 3) provide extensive training for the next generation of bioanalytical chemists in this highly relevant field; 4) further establish Canada’s position as a world leader in proteomics and peptide chromatography research.