Cells were washed in PBS and lysed for 10 min at 99°C in 6 M guanidine-HCl, 100 mM tris (pH 8.5), 5 mM TCEP, and 10 mM CAA, and whole-cell extracts were sonicated. Cell lysates were digested by Lys-C (Wako) and trypsin (Sigma-Aldrich), and resulting peptides were processed by high-pH fractionation (14 fractions per biological replicate; two replicates in total) as described by Batth et al. (75).

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