PXD049386-1

PXD049386 is an original dataset announced via ProteomeXchange.

Title	Carrier protein-enabled host cell proteome analysis (CP-HCP) with integrated isobaric tag interference filtering.
Description	Here, we proposed that the use of an HCP carrier proteome could enhance the acquisition of spectra from HCPs amidst a highly abundance therapeutic protein background to perform global HCP analysis. We provide proof of principle of this approach, which we term carrier proteome-HCP (CP-HCP) analysis, using a basic model of bovine serum albumin (BSA) as a therapeutic protein and BL21 expression strain E.coli as a host cell proteome. We observe that MS3 based methods do not alleviate interference in this model due to the high mock therapeutic background, so we added an interference detection channel to filter co-isolation interference-containing peptides. The approach also does not require any type of enrichment and can identify hundreds of E.coli peptides at small quantities amidst a high background protein.
HostingRepository	PRIDE
AnnounceDate	2026-01-12
AnnouncementXML	Submission_2026-01-11_16:12:17.991.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	J Patrick Murphy
SpeciesList	scientific name: Escherichia coli; NCBI TaxID: NEWT:562; scientific name: Bacteria; NCBI TaxID: NCBITaxon:2;
ModificationList	iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2024-02-14 10:11:54	ID requested
⏵ 1	2026-01-11 16:12:18	announced

Karmani D, Seifihesar N, Sultonova M, Blackmore B, Paulo JA, Harty M, Murphy JP, Carrier-Guided Proteome Analysis in a High Protein Background: An Improved Approach to Host Cell Protein Identification. J Proteome Res, 23(11):5193-5202(2024) [pubmed]

10.1021/acs.jproteome.4c00158;

submitter keyword: Carrier Proteome,Host Cell Proteome, E.coli

Dr. J Patrick Murphy
contact affiliation	Univeristy of Prince Edward Island
contact email	jpmurphy@upei.ca
lab head
J Patrick Murphy
contact affiliation	University of Prince Edward Island
contact email	jpmurphy@upei.ca
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/2026/01/PXD049386

PRIDE project URI

• PRIDE
  1. PXD049386
     1. Label: PRIDE project
     2. Name: Carrier protein-enabled host cell proteome analysis (CP-HCP) with integrated isobaric tag interference filtering.