Optimized MeOH/MTBE-based Protein Precipitation and Lipid Removal Enables High Enrichment of Low Molecular Weight Peptides and Proteins from Human Plasma

ABSTRACT: Low molecular weight (LMW) peptides and proteins (LMWPs, < 30 kDa) in human plasma, serving as potential biomarkers or drug targets, are endowed with a wealth of biological and clinical research values. However, the extraction of LMW species is retarded by high-abundance proteins (HAPs) and therein large dynamic concentration ranges of proteins in plasma. Here we present an optimized MeOH/MTBE-based organic solvent precipitation approach that combining the efficient protein precipitation and effective delipidation (referred here as MeOH/MTBE) to enrich LMWPs from human plasma. The Tricine-SDS-PAGE analysis showed that MeOH/MTBE can not only maximally deplete HAPs but also effectively extract LMWPs from human plasma. By coupling with Top-Down Proteomics (TDP) strategy, MeOH/MTBE enabled the identification of 725 peptides derived from 158 proteins on average from human plasma, which should represent the largest number to our best knowledge with regard to TDP-based single LC-MS/MS acquisition. When combined with Bottom-Up Proteomics (BUP) strategy, MeOH/MTBE allowed for the identification of 376 proteins from human plasma. Notably, 155 out of 376 identified proteins (41.2%) were found to be with a molecular weight under 30 kDa, which further proved the efficient enrichment of LMWPs from human plasma by MeOH/MTBE approach. Moreover, concentrations of the identified proteins were found to span 5-6 orders of magnitude according to the PaxDb dataset. Additionally, many low abundant peptides including 25 neuropeptides and 19 smORF-encoded polypeptides (SEPs) derived from long noncoding RNAs (lncRNAs) were detected. Taken together, the MeOH/MTBE approach described here represents a simple, rapid and reproducible methodology for efficient and sensitive analysis of LMWPs and low abundant proteins from human plasma, which will greatly facilitate the selective identification and quantification of LMWPs from human plasma and accelerate the discovery rate of potential biomarkers and drug targets.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Na Li  

LAB HEAD: Fuquan Yang

PROVIDER: PXD016957 | Pride | 2020-07-07

REPOSITORIES: Pride