as described for the discovery proteomes with two differences: only MS2 scans were obtained and MS2 spectra were searched against the UniProtKB human brain proteome database downloaded in April 2015. A total of 11,518 proteins were quantified. We used the same quality control procedures as the discovery proteomic data to remove proteins with more than 50% missing data, and identify and remove outliers, and remove the effects of clinical covariates (i.e., age, sex, the final clinical diagnosis of cognitive status) from the proteomic profile before estimating the protein weights.
