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

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.

SUBMITTER: Pham TV

PROVIDER: S-EPMC7178409 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics.

Pham Thang V TV Henneman Alex A AA Jimenez Connie R CR

Bioinformatics (Oxford, England) 20200401 8

<h4>Summary</h4>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 separatel ...[more]

PMID: 31909781

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