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

TL;DR

TraianProt is an accessible web-based R Shiny platform that simplifies downstream analysis of proteomics data from various mass spectrometry formats, enabling biological insights without programming expertise.

Contribution

It introduces a comprehensive, user-friendly platform supporting multiple data formats and analysis modules for proteomics data, streamlining the workflow for researchers.

Findings

Supports diverse proteomics data formats and acquisition modes.

Provides customizable visualizations like heatmaps and volcano plots.

Facilitates biological interpretation without programming skills.

Abstract

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