A uniform pipeline is used for all the datasets reanalyzed in iProX. First, all mass spectrometry raw files were converted into mzXML and MGF files using the msconvert module in ProteoWizard. Then the MS/MS peak lists (MGF files) were submitted to a local Mascot server for database searching against the database containing sequences of all human proteins from Uniprot Swiss-Prot. The target-decoy database search strategy was applied. The Decoy checkbox were chosen to perform an automatic decoy database search by MASCOT. The monoisotopic mass was used for both peptide and fragment ions, with fixed modification (Carbamidomethylation, +57.0214 Da) on cysteine and variable modification (Oxidation, +15.9949 Da) on methionine. Tryptic cleavage after Lys or Arg was selected and up to 2 missed cleavage sites were allowed. The precursor and fragment ion mass tolerance are 20 ppm and 0.05 Da for the high-high accuracy data (Q-Exactive, Orbitrap Fusion). PepDistiller was used for quality control to facilitate the validation of MASCOT search results. Peptides length shorter than seven amino acids were removed and all peptide-spectra matches were filtered by the probability value of PepDistiller and Mascot ionscore to keep the FDR measured by the decoy hits lower than 1%.