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Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression

ABSTRACT: Targeted proteomics enables hypothesis-driven research by measuring the cellular expression of protein cohorts related by function, disease, or class after perturbation. Here, we present a pathway-centric approach and an assay builder resource for targeting entire pathways of proteins selected from up to 10,000 expressed proteins to directly measure their abundances, exploiting sample multiplexing to increase throughput by 16-fold. The strategy, termed GoDig, requires only a single-shot LC-MS analysis, ~1 ug combined peptide material, and real-time analytics to trigger simultaneous quantification of up to 16 samples for hundreds of analytes. We applied GoDig to quantify the impact of genetic variation on protein expression in mice fed a high-fat diet. Protein abundances were quantified for multiple protein families (e.g., kinases, lipid metabolism- and lipid droplet-associated proteins) across 480 fully-genotyped Diversity Outbred mice, revealing previously unknown protein quantitative trait loci and establishing potential linkages between specific proteins and lipid homeostasis.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: Steven P Gygi

PROVIDER: MSV000090110 | MassIVE | Thu Aug 11 05:36:00 BST 2022

REPOSITORIES: MassIVE

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Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression.

Yu Qing Q Liu Xinyue X Keller Mark P MP Navarrete-Perea Jose J Zhang Tian T Fu Sipei S Vaites Laura P LP Shuken Steven R SR Schmid Ernst E Keele Gregory R GR Li Jiaming J Huttlin Edward L EL Rashan Edrees H EH Simcox Judith J Churchill Gary A GA Schweppe Devin K DK Attie Alan D AD Paulo Joao A JA Gygi Steven P SP

Nature communications 20230202 1

Targeted proteomics enables hypothesis-driven research by measuring the cellular expression of protein cohorts related by function, disease, or class after perturbation. Here, we present a pathway-centric approach and an assay builder resource for targeting entire pathways of up to 200 proteins selected from >10,000 expressed proteins to directly measure their abundances, exploiting sample multiplexing to increase throughput by 16-fold. The strategy, termed GoDig, requires only a single-shot LC- ...[more]

PMID: 36732331

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