Fig. 6: Application of Mag-Net for the assessment of markers of ADD, related diseases, and controls.

a We used a carefully selected cohort of plasma samples from 40 individuals (10 with ADD, 10 with PDD, 10 with PDCN, and 10 who were HCN). The individual samples, in addition to two different controls, were prepared using Mag-Net. The two pooled plasma samples were prepared four separated times and peptides quantified by data-independent acquisition. One sample was used as a quality control for the quantitative measurements, and the second was prepared as a reference control. b The number of peptides detected when the FDR was controlled on the per-run level (red lines) and on the entire experiment level (light gray). The dark gray represents the number of peptides with a non-zero quantity. c The log2 peptide abundances measured between 4 separate preparations and the measurement of the same quality control sample. The lowest Pearson correlation coefficient between pairs was 0.965. d Effect of different data processing steps on the coefficient of variation of different protein quantities. The top row shows the RAW protein quantities, followed by the quantities with between sample median normalization, and the effect of imputation in the last row.