Characteristics of the AML patients in the study and data quality. (A) Relevant clinical parameters and common genetic findings in TCGA patients selected for this study. (B) Number of proteins detected at above-average abundance (greater than reference pool) for each patient or healthy donor sample compared with the normalized protein abundance of the neutrophil elastase (ELANE) serine protease in each sample (defined by TMT). Similar distributions were noted for the other abundant myeloid serine proteases (cathepsin G [CTSG] and proteinase 3 [PRTN3]). Note that high levels of ELANE are not correlated with reduced numbers of detected proteins, suggesting that tryptic peptides are not being cleaved by endogenous proteases during sample preparation. (C) Number of proteins detected for each sample compared with the normalized protein abundance of ELANE using label-free quantification (LFQ). (D-E) Distribution of gene-wise Spearman correlation between proteomic (TMT) and bulk RNA sequencing data (D) and between LFQ and TMT platforms (E). For both panels D and E, only genes quantifiable by both technologies in at least 20% of AML samples were included in the analysis. Dashed red lines represent median values. (F) Measured protein abundance (TMT) for each of the identified cell surface proteins in patients grouped by the percentage of cells from their presentation marrow sample that displayed the same respective marker using clinical flow cytometry. Protein abundance is calculated based on summed reporter ion intensity, which was normalized and median-centered across TMT plexes to a reference sample. Each protein expression value is then scaled to have a maximum value across all measured samples of 1, and a minimum value of 0, for this display. *P < .05 by 1-sided Mann-Whitney U test between groups. (G) Measured protein abundance (TMT) for each of 4 proteins known to be expressed in only 1 AML subtype. Shown are 3 AMLs with PML-RARA fusions, 4 with CBFB-MYH11 fusions, and 2 with RUNX1-RUNX1T1 fusions; 11 other representative AML samples and 3 healthy adult donor bone marrow samples are shown. HGF and RARA are overexpressed only in PML-RARA–initiated AML, MYH11 is overexpressed only in CBFB-MYH11 initiated AML, and RUNX1T1 is overexpressed only in RUNX-RUNX1T1 AML. ITD, internal tandem duplication; NS, not significant.