ProTN

Description

ProTN is now a Shiny app that provides an integrated pipeline for the complete downstream analysis of proteomics, phospho-proteomics, and interactomics data following peptide quantification. The app features four distinct workflows—proTN, phosproTN, phosproTN with proteome background, and interacTN—each accessible through a separate tab in the application menu. ProTN is compatible with MS-based proteomic experiments processed using Proteome Discoverer and MaxQuant, two of the most widely used platforms for extracting peptide abundances from raw MS spectra. For proteome and interactomics analyses, it also supports input files generated by FragPipe and Spectronaut. Designed to be user-friendly, fast, and comprehensive, ProTN delivers high-quality visualizations and tables to facilitate the biological interpretation of results across a range of experimental setups.

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