Nanoproteomics enables proteoform-resolved analysis of low-abundance proteins in human serum

• Published in: Nature communications Vol. 11; no. 1; pp. 3903 - 12
• Main Authors: Tiambeng, Timothy N., Roberts, David S., Brown, Kyle A., Zhu, Yanlong, Chen, Bifan, Wu, Zhijie, Mitchell, Stanford D., Guardado-Alvarez, Tania M., Jin, Song, Ge, Ying
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 06-08-2020; Nature Publishing Group; Nature Portfolio
• Subjects: 631/443/592/75; 631/45/475; 639/925/350/354; 692/53; 82/16; 82/58; 82/83; Antibodies; Biomarkers; Biomarkers - blood; Blood; Blood Chemical Analysis - methods; Blood Proteins - analysis; Body fluids; Calcium-binding protein; Chemical fingerprinting; Coupling (molecular); Enrichment; Heart; Human serum albumin; Humanities and Social Sciences; Humans; Magnetite Nanoparticles - chemistry; Magnetite Nanoparticles - ultrastructure; Mass spectrometry; Mass Spectrometry - methods; Mass spectroscopy; multidisciplinary; Nanoparticles; Nanotechnology; Protein Processing, Post-Translational; Proteins; Proteome - analysis; Proteomes; Proteomics; Proteomics - methods; Reproducibility; Reproducibility of Results; Science; Science (multidisciplinary); Serum albumin; Serum Albumin, Human - analysis; Troponin; Troponin I; Troponin I - blood
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-020-17643-1

Top-down mass spectrometry (MS)-based proteomics provides a comprehensive analysis of proteoforms to achieve a proteome-wide understanding of protein functions. However, the MS detection of low-abundance proteins from blood remains an unsolved challenge due to the extraordinary dynamic range of the blood proteome. Here, we develop an integrated nanoproteomics method coupling peptide-functionalized superparamagnetic nanoparticles (NPs) with top-down MS for the enrichment and comprehensive analysis of cardiac troponin I (cTnI), a gold-standard cardiac biomarker, directly from serum. These NPs enable the sensitive enrichment of cTnI (<1 ng/mL) with high specificity and reproducibility, while simultaneously depleting highly abundant proteins such as human serum albumin (>10
10
more abundant than cTnI). We demonstrate that top-down nanoproteomics can provide high-resolution proteoform-resolved molecular fingerprints of diverse cTnI proteoforms to establish proteoform-pathophysiology relationships. This scalable and reproducible antibody-free strategy can generally enable the proteoform-resolved analysis of low-abundance proteins directly from serum to reveal previously unachievable molecular details.
Top-down proteomics can provide unique insights into the biological variations of protein biomarkers but detecting low-abundance proteins in body fluids remains challenging. Here, the authors develop a nanoparticle-based top-down proteomics approach enabling enrichment and detailed analysis of cardiac troponin I in human serum.