To obtain deeper coverage of the proteome sample, 50 μg of protein extract from one replicate of experiment 1 was separated via SDS–polyacrylamide gel electrophoresis (PAGE), and 10 gel slices were digested with either endoproteinase Lys-C [1:40 (w/w) in 20 mM ABC (ammonium bicarbonate)] or chymotrypsin [1:40 (w/w) in 50 mM tris (pH 8.0) and 10 mM CaCl2], as described previously (26).

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