TraianProt is an interactive R/Shiny package designed to simplify the downstream analysis of wide-format proteomics data. It provides a modular workflow for processing both label-free and labeled quantitative data obtained from Data-Dependent Acquisition (DDA) or Data-Independent Acquisition (DIA) mass spectrometry experiments. Supported input formats include output from tools such as MaxQuant, MSFragger, DIA-NN, ProteoScape, and Proteome Discoverer.