PXD020617

PXD020617 is an original dataset announced via ProteomeXchange.

Title	Addressing reproducibility challenges in cell culture: the impact of oxylipins contained in fetal calf serum
Description	Reproducibility issues regarding complex in vitro cell culture experiments have been mainly attributed to genetic variations within cell lines. Batch-dependent fetal calf serum variations are well known and also represent relevant influencing factors. However, the molecular constituents mediating such effects remained largely unknown. High resolution mass spectrometry is a powerful tool to identify molecular FCS constituents and investigate their effect on cultured cells. Using a differentiation and inflammatory stimulation protocol on U937 cells we observed FCS batch-dependent variations of secreted cytokines, oxylipins and other inflammatory mediators. In order to detect candidate bioactive molecules contained in FCS, the protein and oxylipin composition of FCS batches was investigated. Remarkably, the protein composition showed some, but much less batch-dependent variation when compared to the oxylipin composition. Efficient uptake of C13-labelled arachidonic acid from medium by U937 macrophages and inflammation-induced release thereof including oxylipin products was evidenced. Balancing out FCS batch-dependent nanomolar concentration differences of two selected oxylipins, 5-HETE and 15-HETE, by spiking experiments, resulted in significant proteome alterations of cultured U937 macrophages indicating PPAR activation. High-resolution microscopy demonstrated HETE-induced formation of peroxisomes, thus independently corroborating the proteome profiling results. In conclusion, the present data demonstrate a strong and previously underappreciated influence of FCS-contained oxylipins on cellular effector functions, thus representing a plausible cause for disturbing reproducibility issues.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:22:33.954.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD020617
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Christopher Gerner
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2020-07-28 17:26:51	ID requested
1	2021-06-01 04:27:49	announced
2	2021-06-01 05:38:58	announced	2021-06-01: Updated project metadata.
⏵ 3	2024-10-22 05:22:34	announced	2024-10-22: Updated project metadata.

10.3390/biom11010113;

Niederstaetter L, Neuditschko B, Brunmair J, Janker L, Bileck A, Del Favero G, Gerner C, Eicosanoid Content in Fetal Calf Serum Accounts for Reproducibility Challenges in Cell Culture. Biomolecules, 11(1):(2021) [pubmed]

10.6019/PXD020617;

submitter keyword: eicosanoids, macrophages,reproducibility issues, cell metabolism

Christopher Gerner
contact affiliation	Department of Analytical Chemistry, University of Vienna
contact email	christopher.gerner@univie.ac.at
lab head
Christopher Gerner
contact affiliation	University of Vienna
contact email	christopher.gerner@univie.ac.at
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD020617
     1. Label: PRIDE project
     2. Name: Addressing reproducibility challenges in cell culture: the impact of oxylipins contained in fetal calf serum