TraianProt: a user-friendly R shiny application for wide format proteomics data downstream analysis

Summary: Mass spectrometry coupled to liquid chromatography (LC-MS/MS) is a powerful technique for the charac-terisation of proteomes. However, the diverse software platforms available for processing the raw proteomics data, each produce their own output format, making the extraction of meaningful and interpretable results a difficult task. We present TraianProt, a web-based, user-friendly proteomics data analysis platform, that enables the analysis of both label-free and labeled data from Data-Dependent or Data-Independent Acquisition mass spectrometry mode support-ing different computational platforms such as MaxQuant, MSFragger, DIA-NN, ProteoScape and Proteome Discoverer output formats. TraianProt provides a dynamic framework that includes several processing modules allowing the user to perform a complete downstream analysis covering the stages of data pre-processing, differential expression analy-sis, functional analysis and protein-protein interaction analysis. Data output includes a wide range of high-quality, cus-tomisable graphs such as heatmap, volcano plot, boxplot and barplot. This allows users to extract biological insights from proteomic data without any programming skills. Availability and implementation: TraianProt is implemented in R. Its code and documentation are available on GitHub at https://github.com/SamueldelaCamaraFuentes/TraianProt along with a step-by-step tutorial incorporated in the repository. Contact: sdelacam@ucm.es Supplementary information: Supplementary data are available at Bioinformatics online