Depletion of Abundant Plasma Proteins and Limitations of Plasma Proteomics

TLDR

The study evaluated how top‑7 and top‑14 immunodepletion affect shotgun proteomic detection of plasma proteins across abundance ranges. The authors used immunoaffinity depletion targeting the top 7 or 14 high‑abundance plasma proteins to improve detection of lower‑abundance proteins in shotgun and targeted proteomics. Immunodepletion produced highly repeatable fractionation, enriched non‑targeted proteins by ~4‑fold, increased protein identifications by 25%, yet only 5–6 % of identifications were low‑abundance proteins and the top 50 proteins still dominated, indicating that even with depletion, untargeted LC‑MS/MS cannot efficiently discover low‑abundance disease biomarkers.

Abstract

Immunoaffinity depletion with antibodies to the top 7 or top 14 high-abundance plasma proteins is used to enhance detection of lower abundance proteins in both shotgun and targeted proteomic analyses. We evaluated the effects of top 7/top 14 immunodepletion on the shotgun proteomic analysis of human plasma. Our goal was to evaluate the impact of immunodepletion on detection of proteins across detectable ranges of abundance. The depletion columns afforded highly repeatable and efficient plasma protein fractionation. Relatively few nontargeted proteins were captured by the depletion columns. Analyses of unfractionated and immunodepleted plasma by peptide isoelectric focusing (IEF), followed by liquid chromatography−tandem mass spectrometry (LC−MS/MS), demonstrated enrichment of nontargeted plasma proteins by an average of 4-fold, as assessed by MS/MS spectral counting. Either top 7 or top 14 immunodepletion resulted in a 25% increase in identified proteins compared to unfractionated plasma. Although 23 low-abundance (<10 ng mL−1) plasma proteins were detected, they accounted for only 5−6% of total protein identifications in immunodepleted plasma. In both unfractionated and immunodepleted plasma, the 50 most abundant plasma proteins accounted for 90% of cumulative spectral counts and precursor ion intensities, leaving little capacity to sample lower abundance proteins. Untargeted proteomic analyses using current LC−MS/MS platforms—even with immunodepletion—cannot be expected to efficiently discover low-abundance, disease-specific biomarkers in plasma.