QARIP

QARIP maps mass-spectrometry-derived peptides to protein transmembrane topology to quantify domain-resolved peptide abundances for analysis of regulated intramembrane proteolysis (RIP).

Key Features:

• Topology-aware peptide mapping: Matches identified peptides to the transmembrane topology of proteins to assign peptides to specific domains.
• Domain-specific quantification: Separately quantifies peptides originating from ectodomains and cytoplasmic domains.
• Quantitative ratio computation: Calculates quantitative ratios for distinct topological domains to enable comparative analysis.
• Mass spectrometry-based comparisons: Supports proteome-wide mass spectrometry-based quantitative comparisons across different biological states.
• RIP substrate identification support: Facilitates identification of substrates of regulated intramembrane proteolysis by topology-resolved peptide quantification.
• Quality control and analysis refinement: Provides domain-resolved metrics to improve quality control and refine quantitative analyses of proteomic RIP datasets.

Scientific Applications:

• Identification of RIP substrates: Proteome-wide detection of candidate substrates for RIP proteases using quantitative MS comparisons.
• Analysis of ectodomain shedding and intramembrane proteolysis: Topology-resolved quantification to study sequential proteolytic events (ectodomain shedding followed by intramembrane proteolysis).
• Study of membrane protein regulation and intercellular communication: Domain-specific abundance changes of membrane proteins to investigate mechanisms of regulation and signaling.

Methodology:

Matches identified peptides from mass spectrometry datasets to protein transmembrane topology, assigns peptides to ectodomain or cytoplasmic domain, and computes quantitative ratios for these topological domains across biological states.