iq: Protein Quantification in Mass Spectrometry-Based Proteomics

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>). It offers additional options for protein quantification using the N most intense fragment ions, using all fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160). In general, the tool can be used to integrate multiple proportional observations into a single quantitative value.

Version: 1.9.12
Depends: R (≥ 2.10)
LinkingTo: Rcpp, RcppEigen
Suggests: knitr, rmarkdown
Published: 2023-12-06
DOI: 10.32614/
Author: Thang Pham ORCID iD [aut, cre, cph, ctb], Alex Henneman ORCID iD [ctb]
Maintainer: Thang Pham <t.pham at>
License: BSD_3_clause + file LICENSE
NeedsCompilation: yes
Citation: iq citation info
In views: Omics
CRAN checks: iq results


Reference manual: iq.pdf
Vignettes: Fast MaxLFQ
iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics


Package source: iq_1.9.12.tar.gz
Windows binaries: r-devel:, r-release:, r-oldrel:
macOS binaries: r-release (arm64): iq_1.9.12.tgz, r-oldrel (arm64): iq_1.9.12.tgz, r-release (x86_64): iq_1.9.12.tgz, r-oldrel (x86_64): iq_1.9.12.tgz
Old sources: iq archive

Reverse dependencies:

Reverse suggests: protti


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