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

Abstract

Mass spectrometry based proteomics enables large-scale identification, quantification, and characterization of proteins, post-translational modifications, and dynamic expression changes, providing critical insights into biological processes and disease mechanisms. However, downstream data analysis remains a significant challenge due to the heterogeneity of datasets, diverse computational platforms, and varying output formats, often requiring advanced expertise. To overcome these barriers, user-friendly, web-based solutions have emerged as essential tools, facilitating accessible, customizable, and reproducible analysis while accelerating discovery in proteomics research. 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, supporting MaxQuant, MSFragger, DIA-NN, ProteoScape, and Proteome Discoverer output formats. TraianProt provides a comprehensive suite of stepwise downstream analysis modules, which includes data filtering, normalization procedures, and missing value imputation strategies. The platform also incorporates robust statistical frameworks for differential expression testing, with peptide-spectrum match level correction, thereby enhancing the reliability of biological interpretations. Beyond quantitative comparisons, TraianProt integrates enrichment analyses to contextualize proteomic changes within functional pathways and interaction network analyses allowing users to extract biological insights from proteomic data without any programming this http URL serves as a comprehensive data analysis tool for proteomic studies, capable of analyzing outputs from main search algorithms without manual reformatting.