Protein Quantification in Mass Spectrometry-Based Proteomics R package iq version 2.0.1 CRAN Task View: Omics (https://CRAN.R-project.org/view=Omics) An implementation of the MaxLFQ algorithm by Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>; Pham et al. 2026 <doi:10.1021/acs.jproteome.5c01038>). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, the median polish algorithm by Tukey (1977, ISBN:0201076160), and a robust linear model. In general, the tool can be used to integrate multiple proportional observations into a single quantitative value. Software Depends: R (>= 2.10) LinkingTo: Rcpp, RcppEigen Suggests: knitr, rmarkdown Thang Pham <t.pham@amsterdamumc.nl> Comprehensive R Archive Network (CRAN) Thang Pham [aut, cre, cph, ctb] (ORCID: <https://orcid.org/0000-0003-0333-2492>), Alex Henneman [ctb] (ORCID: <https://orcid.org/0000-0002-3746-4410>) BSD_3_clause + file LICENSE (https://CRAN.R-project.org/package=iq/LICENSE) 2026-03-21 application/tgz https://CRAN.R-project.org/package=iq doi:10.32614/CRAN.package.iq