Easy 2 nano uplc

The dried immunoprecipitated peptides were resuspend in Buffer A (0.2% Formic Acid, 2% ACN, nanoLC grade 97.8% H₂O) and subjected to proteomic analysis using an EASY II nano-UPLC (Thermo Fisher Scientific) connected on-line to an Orbitrap Elite hybrid mass spectrometer with a nanoelectrospray ion source (Thermo Scientific) using settings similar to those previously described (Porras-Yakushi et al., 2015 (link)). Peptides were separated using a 15 cm silica analytical column with a 75 μm inner diameter packed in-house with reversed phase ReproSil-Pur C_18AQ 3 μm resin (Dr Maisch GmbH, Amerbuch-Entringen, Germany). The flow rate was set to 350 nl/min, using a linear gradient of 2%-32% B (0.2% Formic Acid, 80% ACN, 19.8% nanoLC grade H₂O). Mass spectrometry detectable samples were analyzed on a 159 min gradient, while basic reversed phase immunoprecipitated samples were analyzed on a 90 min gradient. The mass spectrometer was set to collect data in a data-dependent mode, switching automatically between full-scan MS and tandem MS acquisition. All samples were analyzed by ETD and decision tree fragmentation. For ETD fragmentation, the fifteen most intense precursor ions were selected, while the 20 most intense ions were selected for fragmentation using the decision tree method. Data acquisition was managed using Xcalibur 2.0.7 and Tune 2.4 software (Thermo Fisher Scientific).