prolfquapp ─ A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics

Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis () of proteins. As experiments grow in complexity, involving more samples, groups, and identified proteins, interactive differential expression analysis tools become impractical. The addresses this challenge by providing a command-line interface that simplifies , making it accessible to nonprogrammers and seamlessly integrating it into workflow management systems. streamlines data processing and result visualization by generating dynamic HTML reports that facilitate the exploration of differential expression results. These reports allow for investigating complex experiments, such as those involving repeated measurements or multiple explanatory variables. Additionally, supports various output formats, including XLSX files, objects and rank files, for further interactive analysis using spreadsheet software, the Shiny application, or gene set enrichment analysis software, respectively. By leveraging advanced statistical models from the R package, offers a user-friendly, integrated solution for large-scale quantitative proteomics studies, combining efficient data processing with insightful, publication-ready outputs.