PXD000520

PXD000520 is an original dataset announced via ProteomeXchange.

Title	Lysine Methylation Promotes VEGFR-2 Activation and Angiogenesis
Description	We have used a chimeric VEGFR-2 in which the extracellular domain of mouse VEGFR-2 was replaced with the extracellular domain of human CSF-1 receptor. VEGFR-2 was immunoprecipitated with anti-VEGFR-2 antibody from PAE cells ectopically expressing VEGFR-2. The immunoprecipitated proteins were eluted and separated on SDS-PAGE, followed by in-gel chymotrypsin or trypsin digestion. The digested samples were analyzed by nano LC/MS/MS on a Thermo Fisher LTQ Orbitrap XL. The LC-MS/MS data were analyzed using Proteome Discoverer (Thermo Fisher Scientific; Version 1.3.0.339). MS/MS search was carried out using Sequest search algorithm against the sequence of target mouse protein from the UniProtKB database. Search parameters included chymotrypsin as the enzyme with four missed cleavage allowed; methylation at lysine and arginine, phosphorylation of serine, threonine, and tyrosine, alkylation at cysteine, and oxidation of methionine were set as dynamic modifications. Precursor and fragment mass tolerance were set to 5 ppm and 0.8 Da, respectively. The false discovery rate was calculated by enabling the peptide sequence analysis using a decoy database. High confidence peptide identifications were obtained by setting a target false discovery rate threshold of 1% at the peptide level.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:59:31.826.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yan Jiang
SpeciesList	scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monomethylated residue; phosphorylated residue; N6,N6,N6-trimethyl-L-lysine; monohydroxylated residue; dimethylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2013-10-16 01:04:48	ID requested
1	2021-03-04 11:10:25	announced
⏵ 2	2024-10-22 04:59:36	announced	2024-10-22: Updated project metadata.

10.1126/scisignal.2004289;

Hartsough EJ, Meyer RD, Chitalia V, Jiang Y, Marquez VE, Zhdanova IV, Weinberg J, Costello CE, Rahimi N, Lysine methylation promotes VEGFR-2 activation and angiogenesis. Sci Signal, 6(304):ra104(2013) [pubmed]

curator keyword: Biological

submitter keyword: in-gel digestion, LC-MS/MS

Nader Rahimi
contact affiliation	Lysine Methylation Promotes VEGFR-2 Activation and Angiogenesis
contact email	Nader.Rahimi@bmc.org
lab head
Yan Jiang
contact affiliation	Department of Biochemistry
contact email	yanjiang@bu.edu
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/2019/11/PXD000520

PRIDE project URI

• PRIDE
  1. PXD000520
     1. Label: PRIDE project
     2. Name: Lysine Methylation Promotes VEGFR-2 Activation and Angiogenesis