Further Development of the Genome Annotating Proteomic Pipeline

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人类生长和功能是有限的，因为它不会随着时间或组织类型而变化，而且在同一物种的个体之间变化很小。为了真正深入了解生物学和疾病机制，我们需要研究基因组中表达的蛋白质，因为这些分子实际上在体内起作用。由于细胞的蛋白质补体随着时间、组织类型和环境条件的变化而变化巨大，因此开发方法来确定特定样品中存在哪些蛋白质至关重要。蛋白质组学是一门鉴定样品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肽，并用质谱（MS）分析它们来产生特征光谱，该光谱可以与已知存在于基因组中的序列相匹配。由于所收集的质谱数据的复杂性和体积，光谱匹配是一个非常困难的过程。在之前资助的BBSRC项目中，我们开发了基因组注释蛋白质组管道（GAPP），该管道使用分布式计算和先进的算法来自信地识别肽。该系统可通过web （www.gapp.info）免费获得，并且在蛋白质组学社区中已被证明很受欢迎。然而，它可以更容易地从系统中提取生物学相关的结果，并且有一些缺失的功能可以使GAPP更广泛地适用/特别支持单个MS数据和其他物种。本提案的目的是增加这一功能并改进GAPP，扩大用户群体并增加GAPP对这些用户的科学价值。

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 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. This spectral matching is a very difficult process, due to the complexity and volume of MS data collected. In a previously funded BBSRC project, we developed the Genome Annotating Proteomic Pipeline (GAPP) which uses distributed computing and advanced algorithms to confidently identify peptides. This system is freely available via the web (www.gapp.info), and has proven popular within the proteomics community. However, it could be easier to extract biologically relevant results from the system, and there are some missing features which would make GAPP much more widely applicable / particular support for single MS data and other species. The aim of this proposal is to add this functionality and improve GAPP, to widen the user community and increase the scientific value of GAPP to these users.