期刊
JOURNAL OF PROTEOME RESEARCH
卷 19, 期 8, 页码 3340-3351出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jproteome.0c00232
关键词
low-molecular weight proteins and peptides; peptidomics; bottom-up proteomics; SPD; lipoproteins; neuropeptides; smORF-encoded polypeptides
资金
- National Key R&D Program of China [2018YFA0507801]
- National Natural Science Foundation of China [31670185]
Low-molecular weight proteins and peptides (LMWPs, <30 kDa) in human plasma serve as potential biomarkers or drug targets and are endowed with desirable traits for biological and clinical studies. However, the identification of LMWPs from plasma is retarded by high-abundance proteins, high-molecular weight proteins, and lipids. Here, we present a sequential precipitation and delipidation (SPD) method for the efficient enrichment of LMWPs based on methyl-tert-butyl ether/methanol/water systems. The enriched LMWP sample was analyzed by single-shot liquid chromatography-tandem mass spectrometry employing both HCD and EThcD without tryptic digestion, and 725 peptides were identified on average. The LMWP sample was also digested and analyzed using a bottom-up proteomics pipeline, and 289 proteins were identified, of which 129 (44.6%) proteins were less than 30 kDa and lipoprotein-associated proteins were significantly enriched. Additionally, 25 neuropeptides and 19 long noncoding RNA-encoded polypeptides were identified. Taken together, the SPD method shows good sensitivity and reproducibility when compared with other enrichment methods and has great potential for clinical biomarker discovery and application.
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