X-tracker: a generic quantitation tool for MS-based proteomics:

人类基因组计划的完成是近代最伟大的科学成就之一，该计划旨在读取人类的整个DNA“蓝图”。然而，基因组本身所能告诉我们的关于人类如何成长和运作的信息是有限的，因为它不会随着时间或组织类型的变化而变化，同一物种的个体之间的差异也很小。为了真正深入了解生物学和疾病机制，我们需要看看基因组表达的蛋白质，因为这些蛋白质实际上是在人体内进行工作的分子。由于细胞的蛋白质组成随着时间的推移、不同组织类型和对环境条件的反应而变化巨大，开发方法来确定特定样本中存在哪些蛋白质以及数量是至关重要的。蛋白质组学是指识别样本中所有蛋白质的科学。这通常是通过分离蛋白质，将它们分解成更小的多肽，并用质谱仪(MS)分析它们以产生与基因组中已知存在的序列相匹配的特征光谱来实现的。基于同样的技术，已经开发出量化样品中蛋白质数量的方法，无论是相对于其他样品还是绝对的。在以前的项目中，我们已经开发了有助于识别蛋白质并对其进行量化的计算方法。它们分别是基因组注释蛋白质组管道(GAPP)和I-Tracker。然而，有许多定量方法可用，更多的方法正在开发中，但目前还没有一种简单的方法来为许多不同的定量方法同时识别和定量同一包装中的蛋白质。也没有一种简单的方法来修改或增加一个系统的方法来适应特定于一个实验室的技术。这项提议的目的是提供一种满足这一需求的系统，从而促进进行定量蛋白质组学实验，并在整个社区传播新方法。

The completion of the Human Genome Project, which set out to read the entire DNA 'blueprint' for a human being, was one of the greatest scientific achievements of recent times. However, there is a limit to what the genome itself can tell us about how a human being grows and functions, as it does not change according to time or tissue type, and varies little between individuals of the same species. To get a real insight into biology and disease mechanisms, we need to look at the proteins expressed from the genome, as these are the molecules that actually do the work in the body. As the protein complement of a cell varies tremendously over time, between tissue types, and in response to environmental conditions, developing methods to identify which proteins are present, and in what quantities, in a particular sample is crucial. Proteomics is the name given to the science of identifying all the proteins within a sample. This is typically achieved by separating the proteins, breaking them up into smaller peptides, and analysing them with mass spectrometry (MS) to generate a characteristic spectrum which can be matched to a sequence known to exist in the genome. Methods to quantify the amount of proteins in a sample, either in relation to other samples or absolutely, have been developed based around the same technology. In previous projects we have developed computational methods that help to identify proteins and to quantitate them. Respectively, these are the Genome Annotating Proteomic Pipeline (GAPP) and i-Tracker. There are however a number of quantitation methods available and more are being developed, but there is currently no easy way of both identifying and quantifying proteins within the same package for a number of different quantitation methods. Nor is there an easy way to modify or add methods to a system to suit techniques specific to one laboratory. The aim of this proposal is to provide a system that meets this need and thereby to facilitate performing quantitative proteomics experiments and also the dissemination of novel methods throughout the community.