PXD002859

PXD002859 is an original dataset announced via ProteomeXchange.

Title	Optimization of SILAC in human embryonic stem cells
Description	We present a fully defined culture system (adapted Essential8 (E8) medium in combination with vitronectin) for human embryonic stem cells (hESC) that can be used for Stable Isotopic Labeling of Amino aCids (SILAC) purposes. Although a complete incorporation of the labels was observed after 4 days in culture, more than 50 % of all mass spectrometry (MS) precursors displayed a conversion of L-arginine (R) to L-proline (P) or L-glumatate (E) of 40 %. To reduce this arginine conversion, E8 medium was modified by adding (1) L-proline, (2) L-ornithine, (3) Nω-hydroxy-nor-L-arginine (Nor-NOHA) acetate or by (4) lowering the arginine concentration. Inhibition of arginine conversion was best obtained by adding 5mM L-ornithine, followed by 3.5 mM L-proline and by lowering arginine concentration to 99.5 µM. No major changes in the proteome (HDMSE data), pluripotency and cell amount could be observed for these adapted Essential8TM media, although sudden cell death was sometimes observed with the use of 99.5 µM L-arginine. In conclusion, we suggest using 5 mM L-ornithine to reduce arginine conversion.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:25:32.779.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Ellen Scheerlinck
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	methylthiolated residue; 5x(13)C-labeled residue; 6x(13)C labeled residue; monohydroxylated residue; deamidated residue
Instrument	TripleTOF 5600; Synapt G2-S HDMS

Revision	Datetime	Status	ChangeLog Entry
0	2015-09-07 01:46:42	ID requested
1	2016-07-15 10:16:40	announced
⏵ 2	2024-10-22 04:25:34	announced	2024-10-22: Updated project metadata.

10.1002/pmic.201600174;

Scheerlinck E, Van Steendam K, Daled S, Govaert E, Vossaert L, Meert P, Van Nieuwerburgh F, Van Soom A, Peelman L, De Sutter P, Heindryckx B, Dhaenens M, Deforce D, Assessing the impact of minimizing arginine conversion in fully defined SILAC culture medium in human embryonic stem cells. Proteomics, 16(20):2605-2614(2016) [pubmed]

curator keyword: Technical

submitter keyword: culture,SILAC, hESC

Prof. Dr. Dieter Deforce
contact affiliation	Laboratory of Pharmaceutical Biotechnology, Ghent University
contact email	dieter.deforce@ugent.be
lab head
Ellen Scheerlinck
contact affiliation	Ghent University
contact email	ellen.scheerlinck@ugent.be
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/2016/07/PXD002859

PRIDE project URI

• PRIDE
  1. PXD002859
     1. Label: PRIDE project
     2. Name: Optimization of SILAC in human embryonic stem cells