Quast Jan-Philipp, Schuster Dina, Picotti Paola
Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich 8093, Switzerland.
Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich 8093, Switzerland.
Bioinform Adv. 2021 Dec 10;2(1):vbab041. doi: 10.1093/bioadv/vbab041. eCollection 2022.
We present a flexible, user-friendly R package called for comprehensive quality control, analysis and interpretation of quantitative bottom-up proteomics data. protti supports the analysis of protein-centric data such as those associated with protein expression analyses, as well as peptide-centric data such as those resulting from limited proteolysis-coupled mass spectrometry analysis. Due to its flexible design, it supports analysis of label-free, data-dependent, data-independent and targeted proteomics datasets. protti can be run on the output of any search engine and software package commonly used for bottom-up proteomics experiments such as Spectronaut, Skyline, MaxQuant or Proteome Discoverer, adequately exported to table format.
protti is implemented as an open-source R package. Release versions are available via CRAN (https://CRAN.R-project.org/package=protti) and work on all major operating systems. The development version is maintained on GitHub (https://github.com/jpquast/protti). Full documentation including examples is provided in the form of vignettes on our package website (jpquast.github.io/protti/).
我们展示了一个灵活、用户友好的R包，用于对自下而上的定量蛋白质组学数据进行全面的质量控制、分析和解释。protti支持对以蛋白质为中心的数据（如与蛋白质表达分析相关的数据）以及以肽为中心的数据（如有限蛋白酶解耦合质谱分析产生的数据）进行分析。由于其灵活的设计，它支持对无标记、数据依赖、数据独立和靶向蛋白质组学数据集进行分析。protti可以在任何用于自下而上蛋白质组学实验的搜索引擎和软件包（如Spectronaut、Skyline、MaxQuant或Proteome Discoverer）的输出上运行，并能充分导出为表格格式。
protti作为一个开源R包实现。发布版本可通过CRAN（https://CRAN.R-project.org/package=protti）获得，并可在所有主流操作系统上运行。开发版本在GitHub（https://github.com/jpquast/protti）上维护。完整的文档包括示例，以包网站（jpquast.github.io/protti/）上的小插图形式提供。
