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> using least-squares analysis in a comprehensive pipeline for processing proteomics data in data-independent acquisition mode (Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>, and a new algorithm using the conjugate gradient method 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), a robust linear model, and fragment weighting. A new iq format enables the processing of large-scale datasets. In general, the tool can be used to integrate multiple proportional observations into a single quantitative value.

Version:	2.2.0
Depends:	R (≥ 4.0.0)
Suggests:	knitr, rmarkdown, arrow
Published:	2026-11-06
DOI:	10.32614/CRAN.package.iq
Author:	Thang V. Pham [aut, cre, cph], Alex A. Henneman [ctb]
Maintainer:	Thang V. Pham <t.pham at amsterdamumc.nl>
BugReports:	https://github.com/tvpham/iq/issues
License:	BSD_3_clause + file LICENSE
URL:	https://github.com/tvpham/iq
NeedsCompilation:	yes
Citation:	iq citation info
In views:	Omics
CRAN checks:	iq results

Documentation:

Reference manual:	iq.html , iq.pdf
Vignettes:	Fast MaxLFQ (source) iq version 2: the iq format and large-scale protein quantification (source) iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics (source)

Downloads:

Package source:	iq_2.2.0.tar.gz
Windows binaries:	r-devel: iq_2.1.0.zip, r-release: iq_2.1.0.zip, r-oldrel: iq_2.2.0.zip
macOS binaries:	r-release (arm64): iq_2.2.0.tgz, r-oldrel (arm64): iq_2.2.0.tgz, r-release (x86_64): iq_2.2.0.tgz, r-oldrel (x86_64): iq_2.2.0.tgz
Old sources:	iq archive

Reverse dependencies:

Reverse suggests:

msqrob2, protti

Linking:

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