PXD018439

PXD018439 is an original dataset announced via ProteomeXchange.

Title	Time-resolved proteomic profiling for CHO-K1 fed-batch cultivations
Description	The majority of recombinant protein therapeutics are produced with Chinese Hamster Ovary (CHO) cells. Productivity depends on the initial cell line engineering in terms of integration site or choice of an appropriate promotor for the recombinant gene expression, as well as media and process parameter optimization. Here, proteomic profiling is used to identify optimization targets for a pharmaceutical relevant cell line system. Triplicates of CHO-K1 cell 2 L bioreactor fedbatch cultivations were performed and daily sampled for nLC-MS/MS proteomic analysis. Collected data from day 3 up to day 11 showed high Pearson correlation of 93.7 ± 4 % with ca. 2500 proteins quantified. The different growth phases were separated by principal component analysis and hierarchical clustering approaches. Subsequent statistical analysis revealed distinct protein profiles, where steady increase or decrease over time were the most prominent clusters. Fisher exact enrichment tests yielded in significantly enriched protein annotations which were successfully mapped to growth and metabolic changes during fedbatch cell cultivation. Major improvements in cellular and process understanding were achieved and yielded in the identification of promising new targets, like strong endogenous promotors, for cellular engineering and process optimization of this biopharmaceutical relevant cell line.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:18:02.986.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Louise Schelletter
SpeciesList	scientific name: Cricetulus griseus (Chinese hamster) (Cricetulus barabensis griseus); NCBI TaxID: 10029;
ModificationList	monohydroxylated residue; acetylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-04-09 01:12:40	ID requested
1	2021-03-04 13:23:57	announced
⏵ 2	2024-10-22 05:18:03	announced	2024-10-22: Updated project metadata.

10.1002/rcm.8873;

Schelletter L, Hertel O, Antar SJ, Scherling C, L, ä, ttig J, Noll T, Hoffrogge R, A positive pressure workstation for semi-automated peptide purification of complex proteomic samples. Rapid Commun Mass Spectrom, 35(2):e8873(2021) [pubmed]

submitter keyword: Fedbatch cultivation, nLC-MS/MS,CHO, Proteomics, DDA

Thomas Noll
contact affiliation	Cell Culture Technology, Technical Faculty, Bielefeld University, Germany
contact email	thomas.noll@uni-bielefeld.de
lab head
Louise Schelletter
contact affiliation	Bielefeld University
contact email	l.brachtvogel@uni-bielefeld.de
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/2021/01/PXD018439

PRIDE project URI

• PRIDE
  1. PXD018439
     1. Label: PRIDE project
     2. Name: Time-resolved proteomic profiling for CHO-K1 fed-batch cultivations