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MeCN, TFA, MDA MB 231 Cell Line, HTB-26 cell, SDH, magnesium formate, Tumor, Apaf-1, zinc salt, MDA MB 231 Cells, RP11-508D10.1, Bca, SDS, Polypeptides, cobalt(II) formate dihydrate, CH3-C#N, Line, AGM4, cancer of the breast, AGAMOUS-like 61, Leukocyte Adhesion Molecule, Analysis, 7, Work Flow, 9, DiA, BC, bca, type 5 acid phosphatase, C79325, hac-1, Analyses, DIASP, DIA, Dia, AI047805, Dihydrotachysterin, 4-(4-dihexadecylaminostyryl)N-methylpyridium iodide, T-cell antigen Gp39, cancer of breast, scientific observation, ACN, Acn, TNFSF5, Breast Malignant Neoplasms, nickel salt, Tumors, LC-MS2, cobalt (+2) salt, Trypsin/K, Tnfrsf5, anon-53Fa, l(2)SH0173, Spectrum Analysis, hCD40L, Workflows, sodium (4:1:1) salt, Dm1, magnesium salt, IMD3, CG6829, dark/hac-1/dapaf-1, Carcinomas, Intercellular Adhesion Molecule, LY57, F27C12_24, Molecules, NKTL, formate, F27C12.24, Spectrometry, Shwachman-Diamond type metaphyseal dysplasia, cromium (+3), Shwachman syndrome, \"mammary neoplasm\" RELATED [], beta Trypsin, breast cancer, spirit of wood, liquid chromatography-tandem mass spectroscopy, Breast Tumors, Cells, DIANA, Breast Malignant Tumors, ammonium (4:1) salt, orthophosphoric acid, methyl cyanide, lead (+2) salt, cancer, Work Flows, Methyl Alcohol, F10B6_15, MDA-MB-231 Cell Lines, nickel formate dihydrate, Intercellular Adhesion Molecules, lead formate, Ly62, Neoplasms, TAPK, aluminum salt, Mammary Cancers, CH3OH, protein-containing complex, TR-AP, 10alpha, 17alpha)-isomer, F10B6.15, CG7826, Human, Breast Malignant Tumor, MDAMB-231 cell, Breast Tumor, Ly57, GP39, LC-MSMS, Gene Products, CG7835, HILDA, CG42273, breast tumor, gp39, CD154, anatomical systems, CATC4, GKLP, Acinus, thallium (+1) salt, Mammary Neoplasm, ligand, Mammary Carcinoma, beta-Trypsin, rubidium salt, 4733401P19Rik, methanoic acid, Solution, acinusL, PCTAIRE2-binding protein, MGC:45012, Adhesion Molecule, acinusS, Malignant Tumor of Breast, congenital lipomatosis of pancreas, peptidos, Cancer, measuring, 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Neoplasms, lead salt, protein, peptide, Tnfsf5, Leukocyte Adhesion Molecules, ammonium tetraformate, POF, Uni-Etch, peptido, BANF, \"neoplasm of breast (disorder)\" EXACT [SNOMEDCT_2005_07_31:126926005], congenital, Molecule, Min, Apaf1, protein aggregate, ARK, MDA MB 134 Breast Carcinoma Cells, DmelCG42273, wood alcohol, Mass Spectrum Analysis, T-BAM, Mammary Neoplasms, malignant neoplasm of breast, 3-hydroxy-5-estrane-17-carbonitrile, AT-10, (3beta, MS2., tartrate-resistant acid ATPase, LCMSMS, l(2)k07135, peptides, 2610036I19Rik, 2610510L13Rik, Human Mammary Carcinomas, hypoplasia, arc, min, mAPC, copper, ark, T1, lipomatosis of pancreas, TRAP3, fSAP152, Tudor repeat associator with PCTAIRE-2, lithium salt, SOLO DANCERS, 38E.16, HTB26 cell, TF, Shwachman-Bodian syndrome, Lyw-57, dApaf1, TEAB, Sodium Methoxide, T5ap, mammary cancer, MGC - 45012, ammonium (2:1) salt, Concise etchant, CD40L, Carcinoma, \"breast neoplasm\" EXACT [MTH:120], Alcohol, D-Apaf-1, Cd40l, LC-MS/MS, 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22E)-, \"mammary tumor\" EXACT [CSP2005:2016-0671], Wood Alcohol, tiny, CD40-L, Intercellular Adhesion, Mass Spectroscopy, Pro-Mega, Human Mammary, 22-trien-3-ol, dapaf-1, dapaf, dark, calcium formate, Cancer of the Breast, lysate, TEIF, DARK, Trap, wood naphtha, Mammary, Mammary Cancer, protein binding involved in cell adhesion, Leukocyte Adhesion, HIGM1, cromium (+3) salt, DIA2, Breast, dArk, Dapaf-1, mammary tumor, 2-iodo-, sodium formate, C78062, MDA-MB-231, BLNK-S, small, P105, DYRK1, Leukocyte, MDA-MB-231 Cell, nickel formate, 3H-labeled, protein complex, PCTAIRE2BP, Desmoplastic astrocytoma of infancy, Cell Lines, strontium formate, Bp50, apaf1, CG1768, strontium salt, Peptide, Breast Malignant Neoplasm, LC/MS/MS, Mammary Carcinomas, Protein, MLPLI, Dyrk1, Dark, Dias, (3alpha, Dark/Apaf-I, ACETONITRILE, tandem MS, cyanomethane, Mass Spectrum, Breast Neoplasm, PRSS, CC1, Tripcellim, cell adhesion molecule, CGI-97, dApaf-1/DARK/HAC-1, chromic formate, Protein Gene Products, Trypure, concentration, Breast Cancer, wood spirit, calcium salt, Peptid, assay, SCH, dAPAF-1, 3-OHECN"],"additional_accession":[]},"is_claimable":false,"name":"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.","dates":{"publication":"Fri Sep 27 00:00:00 BST 2024"},"accession":"PXD041009","cross_references":{"TAXONOMY":["131567","9606"]}}