Label-free analysis with MaxQuant and bioinformatic analysis of Perseus 

LC-MS/MS raw data files were imported into MaxQuant (version 1.3.0.5) for label-free quantification. The database (uniprot human_151619_20160229.fasta) contained 151,619 sequences and was downloaded on February 29, 2016. Search settings were: Main search ppm: 6; Missed cleavages: 2; MS/MS tolerance ppm: 20; De-Isotopic: TRUE; Enzyme: trypsin; Database uniprot_human_151619_20160229 fasta; Fixed modification: carbamidomethyl (cysteine); Variable modifications: Oxidation (methionine), Acetyl (Protein N-term); Decoy database pattern: reverse; LFQ: TRUE; LFQ min; ratio count: 1: Match between runs: 2 min: Peptide FDR: 0.01; Protein FDR: 0.01. The result files of MaxQuant were loaded into Perseus and processed according to the workflow (Tyanova et al. 2018). Perseus v 1.3.0.4 was used for quality control and statistical processing. All potential contaminants, reverse hits and hits only identified by site were filtered out prior to log2 transformation of the LFQ intensities. Proteins with P values < 0.05 were identified to be statistically significant [19, 20]. The Volcano plots were generated by MaxQuant, and P-values were generated by fold change and significance A/B [21].