MassIVE MSV000101892

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Islet-intrinsic sex differences in inflammatory signaling contribute to autoimmune diabetes susceptibility

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Description

Data-independent acquisition was used for quantitative proteomics analysis (PMID: 37918404). Islets were lysed in 8 M Urea, 50 mM Tris pH 8.0, 75 mM NaCl, with protease inhibitors. Disulfide bonds were reduced with 5 mM DTT, alkylated with 40 mM iodoacetamide. Samples were diluted fourfold with 50 mM Tris HCl (pH 8.0), digested with LysC (1/50 ratio) for 2 h at 25 deg C, then trypsin overnight at 25 deg C. Reactions were quenched with 1% TFA, desalted with C18 plates, and peptide concentrations estimated with BCA. Samples were diluted to 0.1 g/L for LC-MS/MS DIA. Analysis was performed on a Q Exactive HF mass spectrometer, separating peptides on a C18 column connected to an Acquity M-Class Nano UHPLC. Tandem spectra were collected from 400-900 m/z with 10 m/z windows, using 30% collision energy, resolution 70,000. A human Swissprot library was created using DIA-NN, considering fully tryptic peptides with up to two missed cleavages, fixed carbamidomethylation, variable acetylation and oxidation, peptides of 7-30 residues, m/z 400-900, charge 2-4. The library had an FDR of 1%, and DIA data were processed similarly, matching against this library. [doi:10.25345/C5JQ0T864] [dataset license: CC0 1.0 Universal (CC0 1.0)]

Keywords: data independent acquisition ; human islets ; type 1 diabetes ; male vs. female ; estrogen ; DatasetType:Proteomics

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Principal Investigators:
(in alphabetical order) 		Ernesto S. Nakayasu, Pacific Northwest National Laboratory, United States
Submitting User: alchemistmatt
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