Raw data processing

The MS2 spectra were searched with the MaxQuant (v. 1.5.1.2)⁴⁵ against the Uniprot human database (released in June, 2014). Carbamidomethylation of cysteine as a fixed modification and N-acetylation and oxidation of methionine as variable modifications were used for each search. A false discovery rate (FDR) cutoff of 1% was applied at the peptide spectrum match (PSM) and protein levels. An initial precursor mass deviation up to 4.5 ppm and a fragment mass deviation up to 20 ppm were allowed. Protein identification required at least one peptide using the ‘razor plus unique peptides’ setting in MaxQuant⁴⁶. Proteins were quantified using the XIC-based label-free quantification (LFQ) algorithm in MaxQuant⁴⁷. The ‘match between runs’ option was used for nonlinear retention time alignment. The match time window was 0.7 min, and the alignment time window was 20 min.