Engineered nanoparticles enable deep proteomics studies at scale by leveraging tunable nano-bio interactions

被引：52

作者：

Ferdosi, Shadi ^{[1
]}

Tangeysh, Behzad ^{[1
]}

Brown, Tristan R. ^{[1
]}

Everley, Patrick A. ^{[1
]}

Figa, Michael ^{[1
]}

McLean, Matthew ^{[1
]}

Elgierari, Eltaher M. ^{[1
]}

Zhao, Xiaoyan ^{[1
]}

Garcia, Veder J. ^{[1
]}

Wang, Tianyu ^{[1
]}

Chang, Matthew E. K. ^{[2
]}

Riedesel, Kateryna ^{[1
]}

Chu, Jessica ^{[1
]}

Mahoney, Max ^{[1
]}

Xia, Hongwei ^{[1
]}

O'Brien, Evan S. ^{[1
]}

Stolarczyk, Craig ^{[1
]}

Harris, Damian ^{[1
]}

Platt, Theodore L. ^{[1
]}

Ma, Philip ^{[1
]}

Goldberg, Martin ^{[1
]}

Langer, Robert ^{[3
]}

Flory, Mark R. ^{[2
]}

Benz, Ryan ^{[1
]}

Tao, Wei ^{[4
,5
]}

Cuevas, Juan Cruz ^{[1
]}

Batzoglou, Serafim ^{[1
]}

Blume, John E. ^{[1
]}

Siddiqui, Asim ^{[1
]}

Hornburg, Daniel ^{[1
]}

Farokhzad, Omid C. ^{[1
,4
,5
]}

机构：

[1] Seer Inc, Redwood City, CA 94065 USA

[2] Oregon Hlth & Amp Sci Univ, Cedar Ctr, Knight Canc Inst, Portland, OR 97239 USA

[3] MIT, David H Koch Inst Integrat Canc Res, Cambridge, MA 02139 USA

[4] Harvard Med Sch, Ctr Nanomed, Brigham & Womens Hosp, Boston, MA 02115 USA

[5] Harvard Med Sch, Brigham & Womens Hosp, Dept Anesthesiol, Boston, MA 02115 USA

来源：

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA | 2022年 / 119卷 / 11期

关键词：

proteomics; nano-bio interaction; nanoparticle; mass spectrometry; machine learning; BIOMARKER DISCOVERY; PLASMA PROTEOME; PROTEINS; IDENTIFICATION; WORKFLOW; CANCER; CORONA;

D O I：

10.1073/pnas.2106053119

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Deep interrogation of plasma proteins on a large scale is a challenge due to the number and concentration of proteins, which span a dynamic range of over 10 orders of magnitude. Current plasma proteomics workflows employ labor-intensive protocols combining abundant protein depletion and sample fractionation. We previously demonstrated the superiority of multinanoparticle (multi-NP) coronas for interrogating the plasma proteome in terms of proteome depth compared to simple workflows. Here we show the superior depth and precision of a multi-NP workflow compared to conventional deep workflows evaluating multiple gradients and search engines as well as data-dependent and data-independent acquisition. We link the physicochemical properties and surface functionalization of NPs to their differential protein selectivity, a key feature in NP panel profiling performance. We find that individual proteins and protein classes are differentially attracted by specific surface properties, opening avenues to design multi-NP panels for deep interrogation of complex biological samples.

引用

页数：11

共 46 条

[1] Plasma Proteome Profiling Reveals Dynamics of Inflammatory and Lipid Homeostasis Markers after Roux-En-Y Gastric Bypass Surgery [J].