2.6. Database search
All raw data were analyzed by Peaks online (X build
1.7.2022-03-24_170623). The following parameters were used: MS 1
tolerance, 10 ppm; MS2 tolerance, 0.02 Da; and searched database,
UniProt-human database (20,375 entries) for the tumor tissue as well as
HeLa samples. A false discovery rate (FDR) lower than 1% was used as
the cutoff value for the peptide, protein, and propensity score matching
(PSM) identification based on the target decoy strategy.
Carbamidomethylation of cysteine was considered a fixed modification,
and protein N-terminal acetylation, oxidation of methionine, and
deamidation of asparagine and glutamine were considered as variable
modifications.