PXD053035

PXD053035 is an original dataset announced via ProteomeXchange.

Title	Development of an optimized LC-MS workflow for Host Cell Protein characterization to support upstream process development
Description	Host cell proteins (HCPs) co-expressed during the production of biotherapeutics can affect the safety, efficacy and stability of the final product. As such, monitoring HCPs populations and amounts throughout the production and purification process are an essential part of the overall quality control framework. Mass spectrometry (MS)is used as an orthogonal method to enzyme-linked immunosorbent assays (ELISA) for simultaneous identification and quantification of HCPs, particularly for the analysis of downstream processes. In this study, we present an MS-based analytical protocol with improvements in both speed and identification performance that can be implemented for routine analysis to support upstream process development. The protocol adopts a streamlined sample preparation strategy combined with a high-throughput MS analysis pipeline. The developed method identifies and quantifies over 1000 HCPs, including 20 proteins listed as high risk in literature, in a clarified cell culture sample with repeatability and precision shown for digest replicates. In addition, we explore the effects of varying standard spike-ins and changes to the data processing pipeline on absolute quantification estimates of the HCPs, which highlights the importance of standardization for the wider use in industry.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_19:20:20.118.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Janik Seidel
SpeciesList	scientific name: Cricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus); NCBI TaxID: 10029;
ModificationList	acetylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	ZenoTOF 7600

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-12 04:24:49	ID requested
⏵ 1	2025-05-06 19:20:21	announced

10.1021/acs.jproteome.4c00637;

Seidel JD, Condina MR, Klingler-Hoffmann M, Young C, Donnellan L, Kyngdon C, Hoffmann P, Development of an Optimized LC-MS Workflow for Host Cell Protein Characterization to Support Upstream Process Development. J Proteome Res, 24(1):234-243(2025) [pubmed]

submitter keyword: process analytical technologies,Host cell proteins, LC-MS, clarified cell culture fluid, absolute quantification, Chinese hamster ovary, data-independent acquisition, hi3 quantification, bio-processing

Prof. Peter Hoffmann
contact affiliation	Clinical and Health Sciences, Mass Spectrometry and Proteomics facility, University of South Australia, Adelaide, Australia
contact email	Peter.Hoffmann@unisa.edu.au
lab head
Janik Seidel
contact affiliation	University of South Australia (UniSA)
contact email	seijy006@mymail.unisa.edu.au
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/2025/05/PXD053035

PRIDE project URI

• PRIDE
  1. PXD053035
     1. Label: PRIDE project
     2. Name: Development of an optimized LC-MS workflow for Host Cell Protein characterization to support upstream process development