Reproducible protein quantitation of 270 human proteins at increased depth using nanoparticle-based fractionation and reaction monitoring mass spectrometry with stable isotope-labelled internal standards

When using a mix of 274 light synthetic peptide standards as surrogates for 270 human plasma proteins, as well as stable isotope-labelled standards as normalizers for targeted quantitative analysis by LC/MRM-MS, the Seer Proteograph allowed for the enrichment and absolute quantitation of up to an additional 44% of protein targets (median) as well as improved reproducibility compared to a traditional proteomic workflow with no fractionation (median 8.3% vs. 13.1% CV). As the Proteograph technology gains popularity, establishing Proteograph-specific protein reference ranges and comparisons to methods like ELISA and LC/MRM-MS may be explored to enable absolute quantification of plasma proteins based on Proteograph data.