PXD029461

PXD029461 is an original dataset announced via ProteomeXchange.

Title	Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression
Description	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.
HostingRepository	PRIDE
AnnounceDate	2023-11-14
AnnouncementXML	Submission_2023-11-14_08:36:24.212.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Qing Yu
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Eclipse

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-01 05:00:02	ID requested
1	2023-03-10 19:55:31	announced
⏵ 2	2023-11-14 08:36:25	announced	2023-11-14: Updated project metadata.

Yu Q, Liu X, Keller MP, Navarrete-Perea J, Zhang T, Fu S, Vaites LP, Shuken SR, Schmid E, Keele GR, Li J, Huttlin EL, Rashan EH, Simcox J, Churchill GA, Schweppe DK, Attie AD, Paulo JA, Gygi SP, Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression. Nat Commun, 14(1):555(2023) [pubmed]

submitter keyword: sample multiplexing, mouse proteome, TMT,targeted proteomics

Steven Gygi
contact affiliation	Harvard medical school
contact email	steven_gygi@hms.harvard.edu
lab head
Qing Yu
contact affiliation	Harvard Medical School
contact email	qing_yu2@hms.harvard.edu
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2023/03/PXD029461

PRIDE project URI

• PRIDE
  1. PXD029461
     1. Label: PRIDE project
     2. Name: Sample multiplexing-based targeted pathway proteomics with real-time analytics reveals the impact of genetic variation on protein expression