Nanoparticle Enrichment Mass-Spectrometry Proteomics Identifies Protein Altering Variants for Precise pQTL Mapping

Abstract

ABSTRACTGenome-wide association studies (GWAS) with proteomics generate hypotheses on protein function and offer genetic evidence for drug target prioritization. Although most protein quantitative loci (pQTLs) have so far been identified by high-throughput affinity proteomics platforms, these methods also have some limitations, such as uncertainty about target identity, non-specific binding of aptamers, and inability to handle epitope-modifying variants that affect affinity binding. Mass spectrometry (MS) proteomics has the potential to overcome these challenges and broaden the scope of pQTL studies. Here, we employ the recently developed MS-based Proteograph™ workflow (Seer, Inc.) to quantify over 18,000 unique peptides from almost 3,000 proteins in more than 320 blood samples from a multi-ethnic cohort. We implement a bottom-up MS-proteomics approach for the detection and quantification of blood-circulating proteins in the presence of protein altering variants (PAVs). We identify 184 PAVs located in 137 genes that are significantly associated with their corresponding variant peptides in MS data (MS-PAVs). Half of these MS-PAVs (94) overlap withcis-pQTLs previously identified by affinity proteomics pQTL studies, thus confirming the target specificity of the affinity binders. An additional 54 MS-PAVs overlap withtrans-pQTLs (and notcis-pQTLs) in affinity proteomics studies, thus identifying the putatively causalcis-encoded protein and providing experimental evidence for its presence in blood. The remaining 36 MS-PAVs have not been previously reported and include proteins that may be inaccessible to affinity proteomics, such as a variant in the incretin pro-peptide (GIP) that associates with type 2 diabetes and cardiovascular disease. Overall, our study introduces a novel approach for analyzing MS-based proteomics data within the GWAS context, provides new insights relevant to genetics-based drug discovery, and highlights the potential of MS-proteomics technologies when applied at population scale.HighlightsThis is the first pQTL study that uses the Proteograph™(Seer Inc.) mass spectrometry-based proteomics workflow.We introduce a novel bottom-up proteomics approach that accounts for protein altering variants in the detection of pQTLs.We confirm the target and potential epitope effects of affinity binders forcis-pQTLs from affinity proteomics studies.We establish putatively causal proteins for known affinity proteomicstrans-pQTLs and confirm their presence in blood.We identify novel protein altering variants in proteins of clinical relevance that may not be accessible to affinity proteomics.Graphical abstract