Omniquad express

We analyzed the proteomes of 400 postmortem brain samples with dorsolateral prefrontal cortex (dPFC) from the ROS/MAP [3 (link)]. In more details, the digested peptides were labeled with isobaric tandem mass tag (TMT) and subjected to liquid chromatography coupled to mass spectrometry (LC–MS) for sequencing. Genotypes were derived from either whole-genome sequencing or genome-wide genotyping by either the Illumina OmniQuad Express or Affymetrix GeneChip 6.0 platforms [15 (link)]. The quality control process was described in the primary study. Finally, 376 subjects with both proteomic and genetic data passed the quality control for the PWAS.
The eQTL dataset was from the PsychENCODE Consortium covering 1,129,652 eQTLs of 11,120 genes from the prefrontal cortex (PFC) (n = 1387) [4 (link)]. We only included the data of SNPs within 1 MB window around each gene. Genotypes were derived either from genome-wide single nucleotide polymorphisms (SNP) arrays or whole genome sequencing.

The discovery PWAS data were obtained from the dorsolateral prefrontal cortex (dPFC) of postmortem brain tissues from 376 subjects recruited by the Religious Orders Study/Memory and Aging Project (ROS/MAP) [19 (link)]. For proteome sequencing, isobaric tandem mass tag peptide labeling was utilized, and peptides were assessed using liquid chromatography coupled to mass spectrometry (MS) [20 (link)]. Wingo et al. [21 (link)] used Thermo Fisher Scientific’s Proteome Discoverer suite v.2.3 and tandem MS spectra to search against the standard UniProtKB human proteome database, which has 20,338 total sequences, to assign peptide spectral matches. Genotyping was done using whole-genome sequencing or genome-wide genotyping on the Illumina OmniQuad Express or Affymetrix GeneChip 6.0 platforms. Over 8356 proteins having both proteomic and genomic data, among which 1475 protein could find significant cis associations with genetic variation.