Widely Distributed Software for Using Mass Spectrometry to Identify Glycans

描述（由申请人提供）：在过去的50年里，我们对人类生物学和疾病的了解大大增加，主要是由于分子水平的进步。也许最熟悉的例子是通过DNA测序研究基因的能力。但同样重要的是通过了解基因的蛋白质产物来研究基因的功能。研究蛋白质的最常用工具已成为通过质谱法进行蛋白质鉴定。其广泛使用的关键是在20世纪90年代开发的软件，如SEQUEST和Mascot，用于从质谱中自动识别蛋白质。现在人们认识到，如果不考虑蛋白质是如何被修饰的，就不能理解蛋白质的功能。也许所有修饰中最重要的是添加糖，称为糖基化。所有蛋白质中至少有50%是糖基化的，并且这种修饰在疾病中的作用已经被牢固地确立。但目前对糖基化的研究仅限于少数实验室。关键的瓶颈之一是软件-类似于SEQUEST和Mascot等程序，用于从质谱中识别聚糖。这种软件以研究的形式存在。我们建议采用一个名为Cartoonist的版本，并改进其功能和性能，以便能够在非常广泛的实验室中使用。我们将首先与一个小型但多样化的研究小组直接合作，使软件成为他们日常协议的一部分。然后，我们将开始通过多种渠道进行更广泛的分销，包括利用现有的NIH资助的功能性糖组学和复杂碳水化合物研究中心联盟。Cartoonist的关键组件已经存在-它们包括峰值拾取，软件重新校准和自动生成卡通，以及用于判断聚糖（糖）如何解释光谱中的峰值的评分功能。通过与少数实验室的合作，我们将确定如何设计和改进这些组件，以创建一个易于使用且通常有用的软件。这种软件是扩大能够检测和测量糖基化的研究人员库的基本要求，而增加库反过来又是更全面地了解糖基化及其在人类疾病中的作用的要求。 公共卫生相关性：蛋白质经常被聚糖（糖）修饰，这些修饰对人类健康非常重要，例如许多研究表明聚糖有可能成为癌症筛查和监测其治疗的标志物。检测聚糖的主要工具是质谱仪，但解释这些机器的输出需要专家，即使这样也非常繁琐。我们建议建立自动“读取”聚糖质谱的研究软件，并将其开发成任何研究实验室都可以使用的工具，从而消除使用聚糖开发治疗的关键瓶颈。

DESCRIPTION (provided by applicant): Our knowledge of human biology and disease has increased tremendously in the past 50 years, primarily due to advances at the molecular level. Perhaps the most familiar example is the ability to study genes via DNA sequencing. But equally important is the study of the function of genes by understanding their protein products. The most general tool for studying proteins has become protein identification via mass spectrometry. A key to its widespread use was the development in the 1990's of software such as SEQUEST and Mascot for automatically identifying proteins from a mass spectrum. It is now recognized that protein function cannot be understood without also considering how proteins are modified. Perhaps the most important of all modifications is the addition of sugars, referred to as glycosylation. At least 50% of all proteins are glycosylated, and the role of such modifications in disease has been firmly established. But the study of glycosylation is currently limited to a small number of laboratories. One of the key bottlenecks is software - analogs of programs like SEQUEST and Mascot for identifying glycans from a mass spectrum. Such software does exist in research form. We propose to take one version, called Cartoonist, and improve its functionality and performance so that it is capable enough to be used in a very wide set of laboratories. We will do this by first working directly with a small but diverse set of research groups to make the software become part of their everyday protocols. Then we will begin wider distribution though multiple channels, including leveraging the existing NIH-funded Consortium for Functional Glycomics and Complex Carbohydrate Research Center. The key components of Cartoonist already exist - they include peak picking, software recalibration, and automatic generation of cartoons, and scoring functions for judging how well a glycan (sugar) can explain the peaks in a spectrum. Working together with a small number of labs, we will determine how to engineer and refine these components to create an easy-to-use and generally useful piece of software. Such software is an essential requirement for expanding the pool of researchers able to detect and measure glycosylation, and increasing the pool is in turn a requirement for a fuller understanding of glycosylation and its role in human disease. PUBLIC HEALTH RELEVANCE: Proteins are frequently modified by glycans (sugars) and these modifications are very important for human health, for example numerous studies show glycans have the potential to be markers for the screening of cancer and the monitoring its treatment. The primary tool for detecting glycans is the mass spectrometer, but interpreting the output of these machines requires an expert, and even then is very tedious. We propose to build on research software that automatically "reads" glycan mass spectra, and develop it into a tool that can be used by any research laboratory, thus removing a key bottleneck to the development of therapies using glycans.