PXD046865

PXD046865 is an original dataset announced via ProteomeXchange.

Title	Quantitative proteomics analysis of insulin and insulin receptor agonist S597 signaling in rat hepatoma cell line
Description	These data files are collected from Stable Isotope Labeling with Amino acids in Cell culture (SILAC) mass spectrometry (MS)-based proteomics and phospho-proteomics experiments. The rat hepatoma cell line, H4IIE, were exposed to SILAC for at least 14 days in Minimum Essential Medium (MEM) for SILAC added 1% Penicillin/Streptomycin, 10% dialyzed fetal bovine serum for use in SILAC, 1% MEM non-essential amino acids solution, sodium pyruvate, and GlutaMAX. The three SILAC conditions comprised the following three conditions: Light (Lys0,Arg0), medium (Lys4,Arg6), and heavy (Lys8,Arg10). For the phospho-proteome analysis, SILAC H4IIE cells were starved overnight and then stimulated with vehicle (light), insulin (medium), and the partial insulin receptor agonist S597 (heavy) for 5, 15, or 30 minutes. After stimulation, the cells were washed in Dulbecco's Phosphate-Buffered Saline (DPBS) and lysed in Guanidine-HCl added PhosSTOP. Protein concentrations were measured by BCA. Two independent sets of biological replicates were collected. For the first biological replicate, 2 mg of protein from each treatment condition was mixed in a 1:1:1 ratio to give a final protein content of 6 mg and for the second 4 mg from each treatment condition was mixed. For proteome analysis, SILAC H4IIE cells were treated with vehicle (light), insulin (medium), and S597 (heavy) for 24 or 48 hours in regular SILAC medium. For the 48-hour samples, the media was changed after 24 hours of stimulation. Following treatment, the cells were washed in DPBS and lysed with RapiGest, and protein concentrations were measured by BCA. To prepare the proteins for digestion, 200 µg of proteins from each treatment condition was mixed in a 1:1:1 ratio for 3 independent biological replicates.
HostingRepository	PRIDE
AnnounceDate	2025-05-06
AnnouncementXML	Submission_2025-05-06_14:10:27.544.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sarah Jørgensen
SpeciesList	scientific name: Rattus norvegicus (Rat); NCBI TaxID: 10116;
ModificationList	phosphorylated residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-11 07:51:40	ID requested
⏵ 1	2025-05-06 14:10:28	announced

10.1038/s41598-024-77817-5;

J, ø, rgensen SH, Emdal KB, Pedersen AK, Axelsen LN, Kildegaard HF, Demozay D, Pedersen T Å, Gr, ø, nborg M, Slaaby R, Nielsen PK, Olsen JV, Multi-layered proteomics identifies insulin-induced upregulation of the EphA2 receptor via the ERK pathway which is dependent on low IGF1R level. Sci Rep, 14(1):28856(2024) [pubmed]

submitter keyword: Phosphoproteomics,Rat, Insulin, SILAC, Hepatoma, LC-MS/MS

Mads Grønborg
contact affiliation	Department of MS Proteomics at Novo Nordisk A/S in Maaloev, Denmark
contact email	mdgr@novonordisk.com
lab head
Sarah Jørgensen
contact affiliation	Universitry of Copenhagen Novo Nordisk A/S
contact email	sjzq@novonordisk.com
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/PXD046865

PRIDE project URI

• PRIDE
  1. PXD046865
     1. Label: PRIDE project
     2. Name: Quantitative proteomics analysis of insulin and insulin receptor agonist S597 signaling in rat hepatoma cell line