Iq: An R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics

Abstract

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.