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Updated: Dec 31, 2025
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Published on: October 24, 2025
iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics
Thang V Pham1, Alex A Henneman1, Connie R Jimenez1
1OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands.
Summary:
We present an R package called iq to enable accurate protein quantification for label-free data-independent acquisition (DIA) mass spectrometry-based proteomics, a recently developed global approach with superior quantitative consistency. We implement the popular maximal peptide ratio extraction module of the MaxLFQ algorithm, so far only applicable to data-dependent acquisition mode using the software suite MaxQuant. Moreover, our implementation shows, for each protein separately, the validity of quantification over all samples. Hence, iq exports a state-of-the-art protein quantification algorithm to the emerging DIA mode in an open-source implementation.
Availability And Implementation:
The open-source R package is available on CRAN, https://github.com/tvpham/iq/releases and oncoproteomics.nl/iq.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
