PXD041009
PXD041009 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Computational ranking-assisted identification of Plexin-B2 in homotypic and heterotypic clustering of circulating tumor cells in breast cancer |
Description | Mass spectrometry (MS)-based global proteomic data was used to developed a novel computational ranking to assess all cell adhesion molecule candidates in breast cancer. Cell lysate was processed using S-Trap workflow. MDA-MB-231 cell lysate were resuspended by 5% SDS. The protein concentration was measured with BCA protein assay and reduced with 10 mM DTT for 15 mins at 37 °C; subsequently alkylated with 50 mM iodoacetamide at 25 °C for 15 mins in the dark. The samples were acidified by phosphoric acid (the final concentration was 2.5%) and then diluted with six volumes of “binding” buffer (90% methanol; 100 mM triethylammonium bicarbonate, TEAB; pH 7.1). After mixing, the protein solution was loaded to an S-Trap filter from Protifi (Huntington, NY), spun at 10,000 g for 1 min and then the filter was washed with 150 μL of binding buffer 3 times. Proteins were digested with Lys-C (Wako) and sequencing-grade trypsin (Promega, V5117) in the filter at 37 °C for 16 h. To elute peptides, 40 μL of 50 mM TEAB, 40 μL of 0.2% formic acid in H2O, and 40 μL of 50% acetonitrile in H2O were added sequentially. The peptide solutions were pooled for BCA assay to estimate peptides amount. 20 μg of peptides were dried with SpeedVac and stored at −80 °C until LC-MS/MS analysis. Lyophilized peptides were reconstituted in 200 μL of 0.1% TFA with 2% ACN containing 0.01% DDM and analyzed by LC-MS/MS using an Orbitrap Fusion Lumos Tribrid mass spectrometer (Thermo Scientific) connected to a nanoACQUITY UPLC system (Waters) in DIA-MS/MS mode. |
HostingRepository | jPOST |
AnnounceDate | 2024-09-27 |
AnnouncementXML | Submission_2024-09-26_08:00:16.125.xml |
DigitalObjectIdentifier | |
ReviewLevel | Non peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Reta Birhanu Kitata |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: cellular organisms; NCBI TaxID: 131567; |
ModificationList | S-carboxamidomethyl-L-cysteine; alpha-amino acetylated residue; L-methionine sulfoxide; unknown modification |
Instrument | LTQ Orbitrap |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2023-03-21 09:33:52 | ID requested | |
⏵ 1 | 2024-09-26 08:00:16 | announced |
Publication List
Dataset with its publication pending |
Keyword List
submitter keyword: Plexin-B2, circulating tumor cells, breast cancer |
Contact List
Tujin Shi | |
---|---|
lab head | |
Reta Birhanu Kitata | |
contact affiliation | PNNL |
dataset submitter |
Full Dataset Link List
jPOST dataset URI |
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.jpostdb.org/JPST002098/ |