Comprehensive MS-based Protein Quantification

All raw MS files were processed using MaxQuant (version 1.6.1.0) (19 (link)). MS/MS spectra were searched against the Human UniprotKB protein sequence database (December 2014, with 88,657 entries of 20,459 human genes) using the Andromeda search engine (20 (link)). Primary searches were performed using 6 ppm precursor ion tolerance for total protein-level analysis. MS/MS ion tolerance was set at 20 ppm. Cysteine carbamidomethylation was used as a fixed modification. Protein N-acetylation and methionine oxidation are considered variable modifications. Enzyme specificity was set to full tryptic digestion. Peptides with a minimum length of six amino acids and up to two missed cleavages were considered. The required false discovery rate (FDR) was set to 1% at peptide, protein, and modification levels. To maximize the number of quantification events across samples, we enabled the “Match between Runs” options on the MaxQuant platform. The MS proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE (21 (link)) partner repository with the dataset identifier PXD034646. Annotated MS/MS spectra can be accessed through MS-Viewer (22 (link)) (https://msviewer.ucsf.edu/cgi-bin/mssearch.cgi?report_title=MS-Viewer&search_key=bzgazjrsgb&search_name=msviewer) with the following search keys: bzgazjrsgb.