iq-R

iq-R performs accurate protein quantification from label-free data-independent acquisition (DIA) mass spectrometry (DIA-MS) proteomics data by adapting the MaxLFQ algorithm to DIA mode.

Key Features:

• Maximal Peptide Ratio Extraction: Implements a maximal peptide ratio extraction module derived from MaxLFQ to enable protein quantification across multiple samples.
• Extension of MaxLFQ to DIA: Adapts the MaxLFQ algorithm, originally developed for DDA, for use with DIA-mode data.
• Quantification Validity Assessment: Computes an assessment of the validity of quantification for each protein across all samples.

Scientific Applications:

• Biomarker discovery: Supports identification of proteins with reproducible quantitative differences across conditions for biomarker studies.
• Disease progression monitoring: Enables tracking of protein abundance changes across longitudinal or comparative clinical samples.
• Comparative proteomics: Facilitates high-throughput comparative analyses of protein abundances across different biological conditions.

Methodology:

Adapts the MaxLFQ algorithm to DIA mode, implements maximal peptide ratio extraction, and computes per-protein quantification validity across samples.