Campbell Matthew P, Nguyen-Khuong Terry, Hayes Catherine A, Flowers Sarah A, Alagesan Kathirvel, Kolarich Daniel, Packer Nicolle H, Karlsson Niclas G
Biomolecular Frontiers Research Centre, Macquarie University, Sydney, New South Wales, Australia.
Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):108-16. doi: 10.1016/j.bbapap.2013.04.018. Epub 2013 Apr 25.
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.
UniCarb-DB数据库是一个新兴的公共糖组学数据储存库，截至2013年3月，它包含从糖蛋白释放的500多个聚糖串联质谱。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，这些数据集需要具备必要的多样性，以支持开发用于数据存储和分析的准确生物信息学工具。作为一个存档数据库，UniCarb-DB的作用是为糖组学领域的研究人员提供开放访问权限，使其能够获取一个全面的LC MS/MS文库，该文库包含从糖蛋白释放的N-连接和O-连接聚糖，这些聚糖已用糖苷键和跨环裂解离子、保留时间以及相关的实验元数据描述进行了注释。在这里，我们介绍了UniCarb-DB数据提交流程及其在构建作为该数据库一部分的LC-MS/MS聚糖标准文库中的实际应用。在这种情况下，成立了一个由三个实验室组成的独立联盟，对相同的23种市售寡糖标准品进行分析，均采用石墨化碳液相色谱（LC）电喷雾电离（ESI）离子阱质谱的负离子模式。计算了三组数据中每个光谱的点积分数，以此作为衡量在基于文库的光谱匹配和聚糖结构鉴定中使用此类数据集所需可比性的指标。展示了电荷状态、去同位素和阈值水平对输入数据质量的影响。提供特征明确的寡糖裂解数据为识别特定聚糖结构的决定因素提供了机会，并将有助于提高将聚糖结构分配给实验MS/MS光谱的算法的置信度。本文是名为：鉴定后时代的计算蛋白质组学的特刊的一部分。客座编辑：Martin Eisenacher和Christian Stephan。
