Zhou Zhenru, Phung Qui T, Bakalarski Corey E
Department of Proteomic and Genomic Technologies, Genentech, Inc., South San Francisco, CA 94080, United States.
Computational Catalysts, Genentech, Inc., South San Francisco, CA 94080, United States.
Bioinformatics. 2025 Jul 1;41(7). doi: 10.1093/bioinformatics/btaf404.
PepMapViz is a versatile R package that provides flexible peptide mapping and visualization capabilities. PepMapViz can import peptide data output from multiple popular mass spectrometry analysis tools, map peptides to their parent protein sequences, highlight protein domains and modifications, and enable comparative visualization across multiple experimental conditions. Beyond enabling visualization of MHC-presented peptide clusters in different antibody regions to predict potential immunogenicity of antibody-based therapies, PepMapViz can also aid in the visualization of cross-software mass spectrometry results at the peptide level for specific proteins, domain details in a linearized format, and post-translational modification coverage across different experimental conditions.
PepMapViz is freely available on GitHub at https://github.com/Genentech/PepMapViz and on CRAN. The package is implemented in R and includes documentation and example datasets.
PepMapViz是一个多功能的R包，提供灵活的肽段图谱绘制和可视化功能。PepMapViz可以导入多种流行的质谱分析工具输出的肽段数据，将肽段映射到其母蛋白序列，突出显示蛋白结构域和修饰，并能够跨多个实验条件进行比较可视化。除了能够可视化不同抗体区域中MHC呈递的肽段簇以预测基于抗体的疗法的潜在免疫原性外，PepMapViz还可以帮助在肽段水平上可视化特定蛋白质的跨软件质谱结果、线性化格式的结构域细节以及不同实验条件下的翻译后修饰覆盖情况。
PepMapViz可在GitHub上的https://github.com/Genentech/PepMapViz以及CRAN上免费获取。该包用R语言实现，包括文档和示例数据集。
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