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Spectrum raw files were extracted into MS1, MS2, and MS3 (For TMT experiments) files using RawConverter ( The tandem mass spectra were searched against the UniProt human protein database, including isoforms (downloaded on 01-01-2014), and matched to sequences using the ProLuCID/SEQUEST algorithm (ProLuCID version 3.1) with 5 ppm peptide mass tolerance for precursor ions and 600 ppm for fragment ions

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All samples were incubated with primary antibodies overnight at 4 C