Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising 85354, Germany.
Bioinformatics Research Group, University of Applied Sciences Upper Austria, 4232 Hagenberg im Mühlkreis, Austria.
J Proteome Res. 2021 Jun 4;20(6):3388-3394. doi: 10.1021/acs.jproteome.1c00096. Epub 2021 May 10.
Here, we present the Universal Spectrum Explorer (USE), a web-based tool based on IPSA for cross-resource (peptide) spectrum visualization and comparison (https://www.proteomicsdb.org/use/). Mass spectra under investigation can be either provided manually by the user (table format) or automatically retrieved from online repositories supporting access to spectral data via the universal spectrum identifier (USI), or requested from other resources and services implementing a newly designed REST interface. As a proof of principle, we implemented such an interface in ProteomicsDB thereby allowing the retrieval of spectra acquired within the ProteomeTools project or real-time prediction of tandem mass spectra from the deep learning framework Prosit. Annotated mirror spectrum plots can be exported from the USE as editable scalable high-quality vector graphics. The USE was designed and implemented with minimal external dependencies allowing local usage and integration into other web sites (https://github.com/kusterlab/universal_spectrum_explorer).
在这里，我们展示了通用光谱浏览器（USE），这是一个基于 IPSA 的网络工具，用于跨资源（肽）光谱可视化和比较（https://www.proteomicsdb.org/use/）。可通过以下方式提供正在研究的质谱数据：用户手动提供（表格格式），或者从支持通过通用光谱标识符（USI）访问光谱数据的在线存储库自动检索，或者从实现新设计的 REST 接口的其他资源和服务请求。作为原理验证，我们在 ProteomicsDB 中实现了这样的接口，从而允许检索 ProteomeTools 项目中获取的光谱，或从 Prosit 深度学习框架实时预测串联质谱。注释镜像光谱图可以从 USE 中导出为可编辑的、可缩放的高质量矢量图形。USE 的设计和实现具有最小的外部依赖性，允许在本地使用，并集成到其他网站中（https://github.com/kusterlab/universal_spectrum_explorer）。
