Software for automated interpretation of heparan sulfate tandem mass spectra

 描述(申请人提供)：硫酸乙酰肝素串联质谱自动解释软件硫酸乙酰肝素(HS)的表达是胚胎发育和每个生理系统功能所必需的。HS存在于细胞内颗粒、细胞表面和细胞外基质中，与生长因子家族及其受体结合。这些结合作用以细胞类型和发育状态特异性的方式调节细胞对生长因子刺激的反应。将HS结构用作药物开发的挑战在于其生物合成的性质和化学性质。HS链通过一系列酶以非模板驱动的方式在内质网和高尔基体中组装。链首先被聚合，然后受到修饰事件的影响，该事件产生具有被实质上的异质性覆盖的受调节的结构域结构的成熟链。随着HS链生物合成的进行，生物合成酶亚型的数量增加。这些酶，包括60-磺酸转移酶和30-磺酸转移酶，以组织和细胞类型特异性的方式表达，并被认为是以异构体特异性修饰底物。其结果是HS链具有表型特有的结构和蛋白质结合功能。尽管有许多生物合成酶的小鼠突变体可用，但由于缺乏广泛采用的测序方法，HS生物医学的进展受到了阻碍。然而，在过去的几年里，电子激活解离方法(EXD)在质谱学实验室中得到了发展。这些方法，包括电子脱附解离(EDD)和负电子脱附解离(NETD)证明了HS糖的仪器测序的可行性。这些方法的优点是不需要或几乎不需要衍生化，与高通量兼容，并提供丰富的HS糖的结构信息。然而，串联质谱学是高度复杂的，需要量身定做的生物信息学方法来将原始数据转换为序列。我们已经证明了一种算法(HS-SEQ)用于从EXD串联质谱图中对HS糖进行测序的可行性。我们现在建议开发HS-SEQ，以便它能够提供更好的性能和支持自动化HS分析的完整功能，并易于被更广泛的生物医学界使用。未来几年，具有NETD或EDD能力的质谱计的可用性将迅速增长。我们将开发一条数据处理管道，其中包括从原始数据到序列信息的所有必要步骤。这条管道将为熟悉HS生物化学和/或蛋白质组学方法的生物医学科学家设计使用。HS-SEQ管道将作为Web服务运行，并在Creative Commons许可下以源代码和二进制安装程序的形式提供

 DESCRIPTION (provided by applicant): Software for automated interpretation of heparan sulfate tandem mass spectra the expression of heparan sulfate (HS) is required for embryonic development and the functioning of every physiological system. Present in intracellular granules, on cell surfaces and in extracellular matrices, HS binds to growth factor families and their receptors. These binding interactions serve to modulate cellular responses to growth factor stimuli in a cell-type and developmental state specific manner. The challenge to exploitation of HS structures as drugs lies in the nature of their biosynthesis and in their chemical properties. HS chains are assembled in the endoplasmic reticulum and Golgi apparatus by a series of enzymes acting in a non-template driven manner. Chains are first polymerized and then subject to modification events that produce mature chains with a regulated domain structure overlaid by substantial heterogeneity. As the HS chain biosynthesis proceeds, the number of biosynthetic enzymatic isoforms increases. These enzymes, including 6O- sulfotransferases and 3O-sulfotransferases, are expressed in a tissue and cell-type specific manner and are believed to modify substrates with isoform specificity. The result is HS chains that have phenotype-specific structure and protein binding functions. Despite the availability of mouse mutants for many of the biosynthetic enzymes, progress in HS biomedicine has suffered from the lack of widely adopted sequencing methods. Over the past few years, however, electron activated dissociation methods (ExD) have been developed in mass spectrometry laboratories. These methods, including electron detachment dissociation (EDD) and negative electron detachment dissociation (NETD) demonstrate feasibility of instrumental sequencing of HS saccharides. The advantage to these methods is that they require no or minimal derivatization, are compatible with high throughput, and provide rich structural information of the HS saccharides. The tandem mass spectra are highly complex, however, and tailor-made bioinformatics methods are necessary to convert raw data into sequences. We have demonstrated feasibility of an algorithm (HS-SEQ) for sequencing HS saccharide from ExD tandem mass spectra. We now propose to develop HS-SEQ so that it can provide better performance and full features supporting automated HS analysis, and be easily used by the wider biomedical community. The availability of mass spectrometers with NETD or EDD capability will grow rapidly over the next few years. We will develop a pipeline for data processing that includes all steps necessary to go from raw data to sequence information. This pipeline will be designed for use by biomedical scientists familiar with HS biochemistry and/or proteomics methods. The HS- SEQ pipeline will run as a web service and be available in source code and binary installer form under a Creative Commons license