Bilateral BBSRC-NSF/BIO: Bayesian Quantitative Proteomics

细胞中的功能分子是蛋白质——任何给定细胞中特定蛋白质的表达、活性和相互作用决定了细胞的结构和功能。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（MS），它可以计算分子的分子量和丰度。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，称为肽。这一步已经变得很普遍，因为肽更容易用质谱分析，因为它们的质量更低，产生更简单的数据来解释。这个消化步骤的一个挑战是，一些蛋白质分解得很快，而另一些蛋白质消化不完全，产生不可靠的定量数据，这些数据不能被当前的分析软件完全理解或补偿。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开发一套综合分析技术，使用一种强大的统计技术，称为贝叶斯模型。这些进步将被整合到一个免费的软件套件中。串联质谱（MS/MS）和液相色谱（LC）是蛋白质组学中使用的主要技术。最常见的方法是LC分离蛋白质组消化产生的色氨酸片段，然后是串联质谱。整个工作流程被认为是一系列离散的步骤，一些是化学的，一些是仪器的，一些是信息学的，一些是统计的。现有的软件集中于工作流的子组件，并包含一系列确定的、自包含的步骤。该项目将把整个蛋白质定量管道转化为一个严格的统计框架，以贝叶斯方法为基础。新的框架将整合所有实验数据集的证据，并借鉴蛋白质组学工作流程中未使用的结构，包括消化动力学。拟议的管道包括三个协同开发(1)利用所有未确定的（肽）特征，以及已确定的特征，以推断样品中存在的最可能的蛋白质混合物；(2)已知变形形态复杂混合物的差分定量；(3)发现未知的proteoforms及其定量特征所携带的所有修饰（PTMs）。这些进展将首次在变形水平上引起定量灵敏度和解释的阶梯式变化。端到端分析解决方案将在以用户为中心的标准兼容的ProteoSuite包中提供，并作为高通量管道的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.