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.
The Isotopic Ac-IP Tag Enables Multiplexed Proteome Quantification in Data-Independent Acquisition Mode
