Genetic control of the HDL proteome

Nathalie Pamir; Calvin Pan; Deanna L. Plubell; Patrick M. Hutchins; Chongren Tang; Jake Wimberger; Angela Irwin; Thomas Q. de Aguiar Vallim; Jay W. Heinecke; Aldons J. Lusis

Protein quantification. Proteins were quantified using Peptide Spectra Matches (PSM) -the total number of MS/MS spectra detected for a protein (Vaisar et al., 2007) . Proteins considered for analysis had to be detected in ≥30 analyses (%10 of the total samples) with ≥2 unique peptides. Because only a few peptides are typically measured for a given protein, these peptides might not be sufficient to define all isoforms of the protein that are present in the sample therefore, when MS/MS spectra could not differentiate between protein isoforms, the isoform with the most unique peptides was used for further analysis. PSMs for each protein, normalized to either spiked yeast carboxypeptidase or to total PSMs for peptides from each sample, were used to calculate a normalized PSM to compare the relative protein composition of mouse strains' HDLs (Vaisar et al., 2007) . Supplemental Table 1 provides the total calculated PSMs for each protein, the individual peptides that identified each protein, the total number peptide spectra matches, and relative quantification as normalized to yeast carboxypeptidase Y total PSMs or total PSMs of one sample. HDL particle size. HDL particle size was quantified by calibrated ion mobility analysis (Hutchins et al., 2014) . Briefly, HDL isolated by ultracentrifugation from EDTA plasma is introduced into the gas-phase ions by ESI. Because electrophoretic mobility depends chiefly on size, ion mobility analysis data are expressed in terms of particle diameter (nm), which corresponds to the calculated diameter of a singly charged, spherical particle with the same electrophoretic mobility (Hutchins et al., 2014) . Association analyses. GWAS for protein levels and gene expression was performed using correction for population structure as described (Hui et al., 2015; Orozco et al., 2012) . Loci were defined as cis if the peak SNP mapped within 1 Mb of gene position and trans if it mapped outside (cis significance threshold, p < 1.4 e-3; trans threshold, p < 6.13e-6).