Cooperation of GlycoPOST and UniCarb-DR towards a comprehensive glycomics data repository workflow

IF 3.8 2区化学 Q1 BIOCHEMICAL RESEARCH METHODS

Analytical and Bioanalytical Chemistry Pub Date : 2024-11-29 DOI:10.1007/s00216-024-05673-3

Yushi Takahashi, Niclas G. Karlsson, Shujiro Okuda, Kiyoko F. Aoki-Kinoshita

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Abstract

In glycomics, two data repositories, GlycoPOST and UniCarb-DR, have been developed to accumulate experimental data generated by glycomics and glycoproteomics mass spectrometry experiments. In order to enhance the interrelation between these two data repositories, we have upgraded the framework for both of them; we have unified their respective data submission systems and constructed a mechanism that can automatically cross-reference corresponding entries. In addition to this integration, the metadata registration system was also extended so that liquid chromatography experiments can be reported according to standard reporting guidelines specified by MIRAGE (Minimum Information Required for A Glycomics Experiment). Furthermore, by augmenting the visualization software used in UniCarb-DR, we have been able to introduce new functionality into GlycoPOST to enable the visualization of unpublished experimental identification result files during an embargo period defined by the data provider. As a result, this work introduces a new framework by which glycomics researchers can take advantage of GlycoPOST and UniCarb-DR in an integrated manner.

Graphical abstract

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GlycoPOST和UniCarb-DR在糖组学数据存储库工作流程中的合作

在糖组学中，已经开发了两个数据库GlycoPOST和UniCarb-DR，用于积累糖组学和糖蛋白组学质谱实验产生的实验数据。为了增强这两个数据存储库之间的相互关系，我们对它们的框架都进行了升级；我们统一了各自的数据提交系统，并构建了自动交叉引用相应条目的机制。除了这个集成之外，元数据注册系统也得到了扩展，以便可以根据MIRAGE（糖组学实验所需的最低信息）指定的标准报告指南报告液相色谱实验。此外，通过增强UniCarb-DR中使用的可视化软件，我们已经能够在GlycoPOST中引入新功能，以便在数据提供商定义的禁止期间对未发表的实验鉴定结果文件进行可视化。因此，这项工作引入了一个新的框架，通过该框架，糖组学研究人员可以综合利用GlycoPOST和UniCarb-DR。

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来源期刊

Analytical and Bioanalytical Chemistry 化学-分析化学

CiteScore

8.00

自引率

4.70%

发文量

638

审稿时长

2.1 months

期刊介绍： Analytical and Bioanalytical Chemistry’s mission is the rapid publication of excellent and high-impact research articles on fundamental and applied topics of analytical and bioanalytical measurement science. Its scope is broad, and ranges from novel measurement platforms and their characterization to multidisciplinary approaches that effectively address important scientific problems. The Editors encourage submissions presenting innovative analytical research in concept, instrumentation, methods, and/or applications, including: mass spectrometry, spectroscopy, and electroanalysis; advanced separations; analytical strategies in “-omics” and imaging, bioanalysis, and sampling; miniaturized devices, medical diagnostics, sensors; analytical characterization of nano- and biomaterials; chemometrics and advanced data analysis.