Fig. 3

Performance of selected normalization approaches applied to a pool CSF (Set 1) and individual CSF TMT set (Set 2), as evaluated by pepmix TMT ratios and cumulative CV distribution. Following normalization of the pool CSF set (A–E) and individual CSF set (F–J), pepmix TMT ratios at each specified spike-in amount were evaluated separately for all three proteins GPb (green), ADH (red) and enolase (blue). Error bars indicate standard deviation for triplicate measurements. The dotted trendline represents the theoretically expected linear trend of TMT ratios. K, L Summarized mean TMT ratios of all 3 proteins plotted vs. their corresponding spike-in amount for selected normalization approaches (red: no norm., green: QCAL norm., blue: median norm., yellow: Total Peptide Amount norm., brown: quantile norm) applied to the pool CSF sample set (K) and individual CSF sample set (L). M, N Cumulative fraction of proteins below a certain CV in the pool samples set (M) and individual samples set (N) before and after normalization