Validation of the curation pipeline of UniCarb-DB: Building a global glycan reference MS/MS repository
Validation of the curation pipeline of UniCarb-DB: Building a global glycan reference MS/MS repository
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DOI：
10.1016/j.bbapap.2013.04.018
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发表时间：
2014-01-01
影响因子：
3.2
通讯作者：
Karlsson, Niclas G.
中科院分区：
文献类型：
--
作者：
Campbell, Matthew P.;Nguyen-Khuong, Terry;Karlsson, Niclas G.
UniCarb-DB数据库是一个新兴的公共糖组数据储存库，包含500多个(截至2013年3月)从糖蛋白中释放的多糖的串联质谱库。糖组学研究中的一个主要挑战是提供和维护高质量的数据集，这些数据集将提供必要的多样性，以支持用于数据沉积和分析的准确生物信息学工具的开发。作为一个档案数据库，UniCarb-DB的作用是向糖组学社区提供一个全面的LC MS/MS文库，该文库是从糖蛋白中释放的N-和O-连接的糖聚糖，这些糖蛋白已经用糖苷和跨环碎片离子、保留时间和相关的实验元数据描述来注释。在这里，我们介绍了UniCarb-DB数据提交管道及其在构建LC MS/MS多糖标准库方面的实际应用，该库构成了该数据库的一部分。在此背景下，建立了一个由三个实验室组成的独立联合体，以分析相同的23个商用低聚糖标准品，所有这些标准品都在负离子模式下使用石墨化碳液相色谱(LC)电喷雾电离(ESI)离子陷阱质谱仪。为三组数据中的每个光谱计算点积分数，作为在基于库的光谱匹配和多糖结构鉴定中使用这种集合所必需的可比性的衡量标准。给出了电荷态、去同位素和阈值水平对输入数据质量的影响。提供表征良好的寡糖裂解数据提供了识别特定糖链结构的决定因素的机会，并将有助于将糖链结构分配给实验MS/MS谱的算法的置信度。这篇文章是题为：后鉴定时代的计算蛋白质组学特刊的一部分。客座编辑：马丁·艾森纳赫和克里斯蒂安·斯蒂芬。(C)2013爱思唯尔B.V.保留所有权利。
The UniCarb-DB database is an emerging public glycomics data repository, containing over 500 tandem mass spectra (as of March 2013) of glycans released from glycoproteins. A major challenge in glycomics research is to provide and maintain high-quality datasets that will offer the necessary diversity to support the development of accurate bioinformatics tools for data deposition and analySis. The role of UniCarb-DB, as an archival database, is to provide the glycomics community with open-access to a comprehensive LC MS/MS library of N- and O- linked glycans released from glycoproteins that have been annotated with glycosidic and cross-ring fragmentation ions, retention times, and associated experimental metadata descriptions. Here, we introduce the UniCarb-DB data submission pipeline and its practical application to construct a library of LC MS/MS glycan standards that forms part of this database. In this context, an independent consortium of three laboratories was established to analyze the same 23 commercially available oligosaccharide standards, all by using graphitized carbon-liquid chromatography (LC) electrospray ionization (ESI) ion trap mass spectrometry in the negative ion mode. A dot product score was calculated for each spectrum in the three sets of data as a measure of the comparability that is necessary for use of such a collection in library-based spectral matching and glycan structural identification. The effects of charge state, de-isotoping and threshold levels on the quality of the input data are shown. The provision of well-characterized oligosaccharide fragmentation data provides the opportunity to identify determinants of specific glycan structures, and will contribute to the confidence level of algorithms that assign glycan structures to experimental MS/MS spectra. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan. (C) 2013 Elsevier B.V. All rights reserved.