PXD042852

PXD042852 is an original dataset announced via ProteomeXchange.

Title	Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping
Description	Proteogenomics studies generate hypotheses on protein function and provide genetic evidence for drug target prioritization. Most previous work has been conducted using affinity-based proteomics approaches. These technological face challenges, such as uncertainty regarding target identity, non-specific binding, and handling of variants that affect epitope affinity binding. Mass spectrometry (MS)-based proteomics can overcome some of these challenges. Here we report a pQTL study using the Proteograph™ Product Suite workflow (Seer, Inc.) where we quantify over 18,000 unique peptides from nearly 3,000 proteins in more than 320 blood samples from a multi-ethnic cohort in a bottom-up, peptide-centric, MS-based proteomics approach. We identify 184 protein-altering variants (PAVs) in 137 genes that are significantly associated with their corresponding variant peptides, confirming target specificity of co-associated affinity binders, identifying putatively causal cis-encoded proteins and providing experimental evidence for their presence in blood, including proteins that may be inaccessible to affinity-based proteomics.
HostingRepository	PRIDE
AnnounceDate	2023-12-22
AnnouncementXML	Submission_2023-12-21_23:03:58.025.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Karsten Suhre
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Bruker Daltonics timsTOF series

Revision	Datetime	Status	ChangeLog Entry
0	2023-06-09 06:44:42	ID requested
⏵ 1	2023-12-21 23:03:58	announced

Dataset with its publication pending

submitter keyword: Protein altering variants,Proteomics, Protein quantitative trait loci, Mass spectrometry, Genome-wide association studies, Proteograph™ workflow

Karsten Suhre
contact affiliation	Bioinformatics Core, Weill Cornell Medicine-Qatar
contact email	kas2049@qatar-med.cornell.edu
lab head
Karsten Suhre
contact affiliation	Weill Cornell Medicine - Qatar
contact email	kas2049@qatar-med.cornell.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/2023/12/PXD042852

PRIDE project URI

• PRIDE
  1. PXD042852
     1. Label: PRIDE project
     2. Name: Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping