Fig. 3: Boxplots by genotype rs4524 for selected Factor V (F5) protein and peptide intensities.

This figure shows the effect of using the different libraries at the example of the Factor V (F5) protein. Similar plots are provided in Supplementary Fig. 3 and as Source Data with this paper for all 184 MS-PAVs; The boxes are color-coded as following: using the PAV-exclusive library (green), using the reference library (blue), and using the PAV-inclusive library (red). Protein intensities are in dark colors, and peptide intensities are in light colors. The grey horizontal boxplots on top of the plots represent the range of the data shown in that plot compared to the 5–95% range of the entire data for that protein. Units on the y-axis are engine-normalized intensities as provided by DIA-NN. The x-axis labels indicate the number of detected peptides/proteins followed by a colon and the number of samples with the given genotype (order: reference/major allele homozygote, heterozygote, alternate/minor allele homozygote). The first line of the subtitle identifies the protein (Uniprot ID and rsID, when applicable) or the peptide sequence followed by the nanoparticle used in that analysis. The second line shows the number of data points included in generating the plot (N). Significance levels (p-values) for the following hypothesis tests are given: (1) Fisher’s Exact test on detected/non-detected versus presence/absence of the major (p-maj) or minor (p-min) allele, where the stronger of the two associations is shown (indicating MS-PAV detection significance), and (2) a linear regression of peptide intensity versus genotype (coded 0-1-2) with missing values set to zero (pX), and for proteins a linear model including relevant covariates using inverse-normal scaled protein intensities (excluding missing values) against genotype (pY; indicating pQTL significance). Protein name, chromosome, chromosome position (GRCh37), and major and minor alleles are indicated in boldface on top of the boxplots.