GP-Plotter: Flexible Spectral Visualization for Proteomics Data with Emphasis on Glycoproteomics Analysis.

Zheng Fang, Mingming Dong, Hongqiang Qin, Mingliang Ye
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Abstract

Identification evaluation and result dissemination are essential components in mass spectrometry-based proteomics analysis. The visualization of fragment ions in mass spectrum provides strong evidence for peptide identification and modification localization. Here, we present an easy-to-use tool, named GP-Plotter, for ion annotation of tandem mass spectra and corresponding image output. Identification result files of common searching tools in the community and user-customized files are supported as input of GP-Plotter. Multiple display modes and parameter customization can be achieved in GP-Plotter to present annotated spectra of interest. Different image formats, especially vector graphic formats, are available for image generation which is favorable for data publication. Notably, GP-Plotter is also well-suited for the visualization and evaluation of glycopeptide spectrum assignments with comprehensive annotation of glycan fragment ions. With a user-friendly graphical interface, GP-Plotter is expected to be a universal visualization tool for the community. GP-Plotter has been implemented in the latest version of Glyco-Decipher (v1.0.4) and the standalone GP-Plotter software is also freely available at https://github.com/DICP-1809.

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GP-Plotter:灵活的蛋白质组学数据光谱可视化,重点是糖蛋白组学分析。
鉴定评估和结果发布是基于质谱的蛋白质组学分析的重要组成部分。质谱中碎片离子的可视化为多肽的鉴定和修饰定位提供了有力的证据。在此,我们介绍一种名为 GP-Plotter 的易用工具,用于串联质谱的离子注释和相应的图像输出。GP-Plotter 支持社区常用搜索工具的鉴定结果文件和用户自定义文件作为输入。GP-Plotter 可实现多种显示模式和参数定制,以显示感兴趣的注释光谱。不同的图像格式,特别是矢量图形格式,可用于图像生成,这有利于数据发布。值得注意的是,GP-Plotter 还非常适合通过对聚糖片段离子进行全面注释来实现聚糖肽谱分配的可视化和评估。GP-Plotter 具有用户友好的图形界面,有望成为业界通用的可视化工具。GP-Plotter已在最新版的Glyco-Decipher(v1.0.4)中实现,独立的GP-Plotter软件也可在https://github.com/DICP-1809 免费获取。
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