Normalized MassSpec proteome expression values

For mass spectrometry analysis, blood samples were depleted of high abundant blood proteins using the High Select Top14 Abundant Protein Depletion Mini Spin Columns (Thermo Scientific, catalog no A36369) as described by the manufacturer. The total number of samples was analyzed in four separate runs. The four sets were labeled, each set of labeled 16 samples included the same reference sample labeled with TMTpro-126 reagent. The collected peptide fractions were analyzed by LC-MS for peptide/protein identification and quantification. Raw mass spectrometry data was then normalized. The resulting values were log₂ transformed, missing values were set to zero, and then batch corrected for the runs This resulted in data file: sbst4_norm_btchcorrLIMMA_lg2_SIG_MassSpec_2023_260623_2.txt.