*3.2. Plasma Sample Preparations and Development of LC-MS*/*MS*

Four plasma samples were obtained from each of the ten patients, for a total of 40 samples, and their proteins profiled by LC-MS/MS, with each sample assayed in duplicate or triplicate. A total of 1159 proteins were identified, with 684 proteins quantified by more than half and 206 proteins completely quantified in 104 of the LC-MS/MS measurements (Supplementary Table S2). Before comparing plasma protein abundance by the label-free quantification (LFQ) method, six relatively stable and abundant endogenous proteins (BTD, C8B, C1S, ITIH2, IGFALS, and SERPINA3) were chosen for data normalization of the abundance of other proteins, as described in the Materials and Methods section [41,42]. Following normalization of protein abundances in all experiments, sample-to-sample variations were corrected (Supplementary Figure S1A–C). Normalized abundances showed statistically significant correlations with the concentrations of plasma proteins (ng/mL) in the plasma proteome database [43], with a Pearson's correlation coefficient of 0.677 (adjusted *p-*value < 0.001; Supplementary Figure S1D). Assuming technical variations were exceedingly small, only 346 detected proteins measured at one time in each individual sample were considered, followed by the elimination of 24 proteins associated with plasma depletion, including 14 plasma depletion target proteins and

ten immunoglobulin-related proteins, and six normalization factors. A total of 316 proteins were analyzed in the next step, with missing values determined by a least-squares regression approach (Supplementary Table S3) [31,44].