biostudies-literatureUnknown22(4)Wolski WEUniversit?t Z?richMass spectrometry is widely used for quantitative proteomics studies, relative protein quantification, and differential expression analysis of proteins. There is a large variety of quantification software and analysis tools. Nevertheless, there is a need for a modular, easy-to-use application programming interface in <i>R</i> that transparently supports a variety of well principled statistical procedures to make applying them to proteomics data, comparing and understanding their differences easy. The <i>prolfqua</i> package integrates essential steps of the mass spectrometry-based differential expression analysis workflow: quality control, data normalization, protein aggregation, statistical modeling, hypothesis testing, and sample size estimation. The package makes integrating new data foJournal of proteome research1092-1104https://www.ebi.ac.uk/biostudies/studies/S-EPMC10088014biostudies-literature<i>prolfqua</i>: A Comprehensive <i>R</i>-Package for Proteomics Differential Expression Analysis.PMC10088014d'Errico MSchlapbach RWolski WENanni PGrossmann JPanse Cfalse<i>prolfqua</i>: A Comprehensive <i>R</i>-Package for Proteomics Differential Expression Analysis.Mass spectrometry is widely used for quantitative proteomics studies, relative protein quantification, and differential expression analysis of proteins. There is a large variety of quantification software and analysis tools. Nevertheless, there is a need for a modular, easy-to-use application programming interface in <i>R</i> that transparently supports a variety of well principled statistical procedures to make applying them to proteomics data, comparing and understanding their differences easy. The <i>prolfqua</i> package integrates essential steps of the mass spectrometry-based differential expression analysis workflow: quality control, data normalization, protein aggregation, statistical modeling, hypothesis testing, and sample size estimation. The package makes integrating new data fo2023-01-01T00:00:00Z2023 Apr2026-05-29T05:27:33.485Z2026-05-16T03:07:30.315ZS-EPMC100880143693968710.1021/acs.jproteome.2c00441