PXD041009-1

PXD041009 is an original dataset announced via ProteomeXchange.

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

Revision	Datetime	Status	ChangeLog Entry
0	2023-03-21 09:33:52	ID requested
⏵ 1	2024-09-26 08:00:16	announced

Dataset with its publication pending

submitter keyword: Plexin-B2, circulating tumor cells, breast cancer

Tujin Shi
lab head
Reta Birhanu Kitata
contact affiliation	PNNL
dataset submitter

jPOST dataset URI

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