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Chunk #21 — Materials and Methods — Nano-LC-MS/MS Analysis

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A multi-omic analysis of the dorsal striatum in an animal model of divergent genetic risk for alcohol use disorder.
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Nano-LC-MS/MS analyses were performed on an EASY-nLC™ HPLC system (SCR: 014993, Thermo Fisher Scientific) coupled to Orbitrap Fusion™ Lumos™ mass spectrometer (Thermo Fisher Scientific). One third of each fraction was loaded onto a reversed phase EasySprayTM C18 column (2 μm, 100 Å, 75 μm x 50 cm, Thermo Scientific Cat No: ES802A) at 400 nL/min. Peptides were eluted from 4–28% with mobile phase B (Mobile phases A: 0.1% FA, water; B: 0.1% FA, 80% Acetonitrile (Fisher Scientific Cat No: LS122500)) over 160 minutes; 28%−35% B over 5 mins; 35–50% B for 14 minutes; and dropping from 50–10% B over the final 1 min. The mass spectrometer method was operated in positive ion mode with a 4 sec cycle time data-dependent acquisition method with advanced peak determination and Easy-IC (internal calibrant). Precursor scans (m/z 400–1750) were done with an orbitrap resolution of 120000, RF lens% 30, maximum inject time 50 ms, standard AGC target, including charges of 2 to 6 for fragmentation with 60 sec dynamic exclusion. MS2 scans were performed with a fixed first mass of 100 m/z, 34% fixed