Bilateral BBSRC-NSF/BIO: Bayesian Quantitative Proteomics

细胞中的功能分子是蛋白质--特定蛋白质在任何特定细胞中的表达、活性和相互作用决定了它的结构和它能做什么。用于大规模研究蛋白质的技术统称为蛋白质组学。蛋白质组学中使用的主要方法是质谱仪(MS)，它可以计算分子的相对分子质量和丰度。大多数蛋白质组学工作流程在MS之前执行蛋白质消化步骤。消化的结果是所有蛋白质都被分解成小链，称为多肽。这一步骤已经变得很常见，因为多肽更容易被MS分析，因为它们的质量较低，产生的数据更容易解释。在这个消化步骤中的一个挑战是，一些蛋白质迅速分解，而另一些蛋白质的消化是不完整的，产生了不可靠的量化数据，当前的分析软件无法完全理解或弥补这些数据。为了克服这个问题，德克萨斯大学安德森癌症中心将与英国曼彻斯特大学合作，利用一种名为贝叶斯建模的强大统计技术开发一套集成的分析技术。这些改进将被整合到免费提供的软件套件中。串联质谱仪(MS/MS)与液相色谱(LC)联用是蛋白质组学研究的主要手段。最常见的方法是用LC分离来自蛋白质组消化的胰酶片段，然后串联MS多肽。整个工作流程被设想为一系列离散的步骤，一些是化学的，一些是工具的，一些是信息学的，还有一些是统计的。现有软件集中在工作流子组件上，并包括一系列确定的、自包含的步骤。该项目将把整个蛋白质量化管道转化为以贝叶斯方法为基础的严格的统计框架。新的框架将整合所有实验获得的数据集的证据，并从蛋白质组学工作流程中未使用的结构中借用力量，包括消化动力学。拟议的管道由三个协同发展组成：(1)利用所有未鉴定的(肽)特征以及已鉴定的特征来推断样品中存在的最可能的蛋白质混合物；(2)对已知蛋白质形式的复杂混合物进行差异量化；(3)发现未知蛋白质形式及其量化特征所携带的所有修饰(PTM)。这些进展将第一次在蛋白质形式水平上引起量化、灵敏度和解释的阶梯变化。端到端分析解决方案将在符合用户中心标准的ProteoSuite包中提供，并作为高吞吐量管道的Galaxy工作流程。

The functional molecules in cells are proteins - the expression, activity and interactions of particular proteins in any given cell define its structure and what it is capable of doing. The technologies used to study proteins on a large scale are collectively called proteomics. The main method used in proteomics is mass spectrometry (MS), which can calculate the molecular weight and abundance of molecules. The majority of proteomics workflows perform a step of protein digestion prior to MS. The result of digestion is that all the proteins become broken up into small chains, called peptides. This step has become common, because peptides are easier to analyse by MS, due to their lower mass, producing simpler data to interpret. One challenge in this digestion step is that some proteins break down quickly whereas for others digestion is incomplete, producing unreliable quantification data that are not fully understood or compensated for by current analysis software. To overcome this problem, the University of Texas Anderson Cancer Center will collaborate with the University of Manchester in the United Kingdom to develop an integrated suite of analysis techniques using a powerful statistical technique called Bayesian modelling. These advances will be incorporated into a freely available software suite. Tandem Mass Spectrometry (MS/MS) coupled to Liquid Chromatography (LC) is the primary technique used in proteomics. The most common approach is LC separation of tryptic fragments derived from a proteome digestion, followed by tandem MS of the peptides. This entire workflow is conceived as a series of discrete steps, some chemical, some instrumental, some informatics and some statistical. Existing software concentrates on subcomponents of the workflow, and comprise a series of deterministic, self-contained steps. This project will translate the whole protein quantification pipeline into a rigorous statistical framework underpinned by Bayesian methodology. The new framework will integrate evidence across all experimentally acquired datasets, and borrow strength from unused structure within a proteomics workflow, including digestion dynamics. The proposed pipeline consists of three synergistic developments (1) Utilization of all unidentified (peptide) features, as well as identified features, to infer the most likely mixture of proteins present in a sample; (2) Differential quantification of complex mixtures of known proteoforms; (3) Discovery of unknown proteoforms and all modifications (PTMs) carried by their quantification signatures. These advancements will elicit a step-change in quantification sensitivity and interpretation at the proteoform level for the first time. The end-to-end analysis solution will be made available within the user-centric standards compliant ProteoSuite package, and as a Galaxy workflow for high-throughput pipelines.