质谱数据检测和质量检查工具

IF 7.1 2区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY
Todor Kondić, Anjana Elapavalore, Jessy Krier, Adelene Lai, Hiba Mohammed Taha, Mira Narayanan, Emma L. Schymanski
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引用次数: 0

摘要

Shinyscreen是一个基于R包和基于shine的web应用程序,专为高分辨率质谱仪器的原始数据的探索,可视化和质量评估而设计。其多功能的基于列表的方法支持从已知或“可疑”化合物(基于化合物列表的筛选)或检测到的质量(基于质量列表的筛选)开始的数据管理,使其适应不同的分析需求(目标、可疑或非目标筛选)。shinysscreen可以在多种模式下运行,包括作为R包、交互式命令行工具、自文档web GUI或网络可部署服务。Shinyscreen已应用于环境研究、数据库丰富和教育活动,显示了其广泛的用途。Shinyscreen在Apache License 2.0下可在GitLab (https://gitlab.com/uniluxembourg/lcsb/eci/shinyscreen)中获得。存储库包含部署和使用的详细说明。此外,还有一个预先配置的Docker映像,专为无缝安装和操作而设计,主存储库中也提供了说明。科学贡献:shinysscreen是一个完全开源的预筛选应用程序,可帮助分析人员对高分辨率质谱实验中检测到的数千个峰进行高通量质量控制。作为一个独立于供应商、跨操作系统的应用程序,它覆盖了开放质谱工作流程中的一个重要领域。Shinyscreen支持数据的质量控制,以进一步识别或将光谱上传到公共数据资源,以及教学工作,以教育学生数据质量控制和严格识别方法的重要性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Shinyscreen: mass spectrometry data inspection and quality checking utility
Shinyscreen is an R package and Shiny-based web application designed for the exploration, visualization, and quality assessment of raw data from high resolution mass spectrometry instruments. Its versatile list-based approach supports the curation of data starting from either known or “suspected” compounds (compound list-based screening) or detected masses (mass list-based screening), making it adaptable to diverse analytical needs (target, suspect or non-target screening). Shinyscreen can be operated in multiple modes, including as an R package, an interactive command-line tool, a self-documented web GUI, or a network-deployable service. Shinyscreen has been applied in environmental research, database enrichment, and educational initiatives, showcasing its broad utility. Shinyscreen is available in GitLab ( https://gitlab.com/uniluxembourg/lcsb/eci/shinyscreen ) under the Apache License 2.0. The repository contains detailed instructions for deployment and use. Additionally, a pre-configured Docker image, designed for seamless installation and operation is available, with instructions also provided in the main repository. Scientific Contribution: Shinyscreen is a fully open source prescreening application to assist analysts in the high throughput quality control of the thousands of peaks detected in high resolution mass spectrometry experiments. As a vendor-independent, cross operating system application it covers an important niche in open mass spectrometry workflows. Shinyscreen supports quality control of data for further identification or upload of spectra to public data resources, as well as teaching efforts to educate students on the importance of data quality control and rigorous identification methods.
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来源期刊
Journal of Cheminformatics
Journal of Cheminformatics CHEMISTRY, MULTIDISCIPLINARY-COMPUTER SCIENCE, INFORMATION SYSTEMS
CiteScore
14.10
自引率
7.00%
发文量
82
审稿时长
3 months
期刊介绍: Journal of Cheminformatics is an open access journal publishing original peer-reviewed research in all aspects of cheminformatics and molecular modelling. Coverage includes, but is not limited to: chemical information systems, software and databases, and molecular modelling, chemical structure representations and their use in structure, substructure, and similarity searching of chemical substance and chemical reaction databases, computer and molecular graphics, computer-aided molecular design, expert systems, QSAR, and data mining techniques.
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