Example datasets used to demonstrate the R package tidyproteomics.

The analysis presented in this document is use to demo the code for the R package tidyproteomics. The underlying data is based on previously published and publicly available data [1]. Raw data was analyzed using ProteomeDiscoverer 2.5, FragPipe 19.1, and MaxQuant 1.6.10.43 with basic settings for mass tolerance and PTMs. The exported results are provided here. Tidyproteomics is a suite of tools designed to facilitate the analysis of proteomics data with a focus on reproducibility and transparency. The project aims to provide a user-friendly platform for proteomics data analysis. To achieve this, tidyproteomics has been developed using open-source software and is available for anyone interested in proteomics analysis. The platform offers a range of analysis tools, including data pre-processing, normalization, visualization, and statistical analysis.1. Wang, Feng, Shan Li, Nadia Houerbi, and Tsui-Fen Chou. 2022. "Temporal Proteomics Reveal Specific Cell Cycle Oncoprotein Downregulation by p97/VCP Inhibition." Cell Chemical Biology 29 (3): 517–29.e5.