Fig. 3

Proteomic characterization of three different NPs, depleted plasma and neat plasma. A The numbers of protein groups measured via five different plasma proteomic methods, namely, in plasma treated with the three NPs, depleted plasma and neat plasma, as determined by LC‒MS/MS and DIA-NN (version 1.8.1, 1% protein and peptide FDR). M158/M909/M086: protein groups in the samples incubated with the corresponding NPs. Depleted: the protein group in plasma depleted by Thermo Fisher Scientific High-Select™ Top14 Abundant Protein Depletion Resin. Neat Plasma: the protein group of untreated plasma samples. B Coefficients of variation (CVs) of the proteins quantified by the five different methods. Inner boxplots represent the 25% (lower hinge), 50%, and 75% (upper hinge) quantiles. Whiskers indicate observations at or outside the hinge ± 1.5 * interquartile range (IQR). C Correlation of the median of the measured protein intensities with the published protein concentration in the HPA database. The blue lines are linear regression lines, and the grey shaded regions represent the 95% confidence intervals. D Percent coverage of the HPA database for each method (top) and relative coverage of the plasma protein database by the M086-based NP method compared to the neat plasma method (bottom) over negative log10 protein intensities. Only protein groups with complete measurements were kept. All proteins and peptides were filtered with a 1% protein and peptide false discovery rate (FDR). E Rank distribution of the protein groups identified by M086. Ranks by intensity and log10 intensity are shown on the X and Y axes, respectively. Light blue circles represent proteins in the HPA plasma protein database, and dark blue circles represent proteins that were uniquely identified via the M086 method. F UpSet plot showing the overlap of the measured protein groups between the different methods. Only protein groups with complete measurements were kept