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- Title
iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics.
- Authors
Pham, Thang V; Henneman, Alex A; Jimenez, Connie R
- Abstract
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.
- Publication
Bioinformatics, 2020, Vol 36, Issue 8, p2611
- ISSN
1367-4803
- Publication type
Article
- DOI
10.1093/bioinformatics/btz961