Dataset Information

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

ABSTRACT: Targeted proteomics plays a specialized role in hypothesis-driven research where the expression of cohorts of dozens of proteins related by function, disease, co-expression, localization, or class are measured after perturbing a pathway. Moreover, a major advance in proteomics is the ability to combine many samples (up to 16) for simultaneous quantification using tandem mass tag (TMT) reagents. Here we present a pathway-centric approach for targeting protein lists selected from up to 10,000 expressed proteins to directly measure their abundances, exploiting sample multiplexing to increase throughput. The strategy, termed GoDig, requires only a single-shot LC-MS analysis, ~1 µg combined peptide material, and real-time analytics to trigger simultaneous quantification of up to 16 samples for hundreds of analytes. We applied GoDig to investigate the impact of genetic variation on protein expression in mice fed a Western-style diet high in fat and sucrose. For selected sets of proteins of interest (e.g., kinases, lipid metabolism- and lipid droplet-associated proteins), protein abundances from mouse livers from 480 fully genotyped Diversity Outbred mice were profiled. The results revealed previously unknown protein quantitative trait loci (QTL) and established potential linkages between specific proteins and lipid homeostasis. In all, GoDig provides an integrated solution for next-generation targeted pathway proteomics.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Mus Musculus (mouse)

TISSUE(S): Liver

SUBMITTER: Qing Yu

LAB HEAD: Steven Gygi

PROVIDER: PXD029461 | Pride | 2023-03-11

REPOSITORIES: Pride

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			Action	DRS
	502836_ea05273_DOFounder_BioRep3_SetA_90min.mzIdentML	Mzid
	502837_ea05274_DOFounder_BioRep3_SetA_90min.mzIdentML	Mzid
	502838_ea05275_DOFounder_BioRep3_SetA_90min.mzIdentML	Mzid
	502839_ea05276_DOFounder_BioRep3_SetA_90min.mzIdentML	Mzid
	502840_ea05277_DOFounder_BioRep3_SetA_90min.mzIdentML	Mzid

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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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