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

作者：Witold Wolski, Jonas Grossmann, Leonardo Schwarz, Peter Leary, Can Türker, Paolo Nanni, Ralph Schlapbach, Christian Panse · 发表于：Journal of Proteome Research · 年份：2025 · DOI：10.1021/acs.jproteome.4c00911 · 被引用次数：4 · 研究领域：Advanced Proteomics Techniques and Applications、Bioinformatics and Genomic Networks、Gene expression and cancer classification

High Resolution Image Download MS PowerPoint Slide Mass spectrometry is a cornerstone of quantitative proteomics, enabling relative protein quantification and differential expression analysis ( DEA ) of proteins. As experiments grow in complexity, involving more samples, groups, and identified proteins, interactive differential expression analysis tools become impractical. The prolfquapp addresses this challenge by providing a command-line interface that simplifies DEA, making it accessible to nonprogrammers and seamlessly integrating it into workflow management systems. Prolfquapp 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, prolfquapp supports various output formats, including XLSX files, SummarizedExperiment objects and rank files, for further interactive analysis using spreadsheet software, the exploreDE Shiny application, or gene set enrichment analysis software, respectively. By leveraging advanced statistical models from the prolfqua R package, prolfquapp offers a user-friendly, integrated solution for large-scale quantitative proteomics studies, combining efficient data processing with insightful, publication-ready outputs.