Nanodroplet processing platform for deep and quantitative proteome profiling of 10-100 mammalian cells

被引：435

作者：

Zhu, Ying ^{[1
]}

Piehowski, Paul D. ^{[2
]}

Zhao, Rui ^{[1
]}

Chen, Jing ^{[3
]}

Shen, Yufeng ^{[2
]}

Moore, Ronald J. ^{[2
]}

Shukla, Anil K. ^{[2
]}

Petyuk, Vladislav A. ^{[2
]}

Campbell-Thompson, Martha ^{[3
]}

Mathews, Clayton E. ^{[3
]}

Smith, Richard D. ^{[2
]}

Qian, Wei-Jun ^{[2
]}

Kelly, Ryan T. ^{[1
]}

机构：

[1] Pacific Northwest Natl Lab, Environm Mol Sci Lab, Richland, WA 99354 USA

[2] Pacific Northwest Natl Lab, Div Biol Sci, Richland, WA 99354 USA

[3] Univ Florida, Dept Pathol Immunol & Lab Med, Gainesville, FL 32611 USA

来源：

NATURE COMMUNICATIONS | 2018年 / 9卷

基金：

美国国家卫生研究院;

关键词：

MASS-SPECTROMETRY; COMPUTATIONAL PLATFORM; SHOTGUN PROTEOMICS; DROPLET ARRAY; RNA-SEQ; HETEROGENEITY; DIGESTION; PROTEINS; TISSUES; SAMPLE;

D O I：

10.1038/s41467-018-03367-w

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：

Nanoscale or single-cell technologies are critical for biomedical applications. However, current mass spectrometry (MS)-based proteomic approaches require samples comprising a minimum of thousands of cells to provide in-depth profiling. Here, we report the development of a nanoPOTS (nanodroplet processing in one pot for trace samples) platform for small cell population proteomics analysis. NanoPOTS enhances the efficiency and recovery of sample processing by downscaling processing volumes to <200 nL to minimize surface losses. When combined with ultrasensitive liquid chromatography-MS, nanoPOTS allows identification of similar to 1500 to similar to 3000 proteins from similar to 10 to similar to 140 cells, respectively. By incorporating the Match Between Runs algorithm of MaxQuant, >3000 proteins are consistently identified from as few as 10 cells. Furthermore, we demonstrate quantification of similar to 2400 proteins from single human pancreatic islet thin sections from type 1 diabetic and control donors, illustrating the application of nanoPOTS for spatially resolved proteome measurements from clinical tissues.

引用

页数：10

共 44 条

[1] High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin [J].

Achim, Kaia ;

Pettit, Jean-Baptiste ;

Saraiva, Luis R. ;

Gavriouchkina, Daria ;

Larsson, Tomas ;

Arendt, Detlev ;

Marioni, John C. .

NATURE BIOTECHNOLOGY, 2015, 33 (05) :503-U215

[2] Single-Cell Mass Cytometry of Differential Immune and Drug Responses Across a Human Hematopoietic Continuum [J].

Bendall, Sean C. ;

Simonds, Erin F. ;

Qiu, Peng ;

Amir, El-ad D. ;

Krutzik, Peter O. ;

Finck, Rachel ;

Bruggner, Robert V. ;

Melamed, Rachel ;

Trejo, Angelica ;

Ornatsky, Olga I. ;

Balderas, Robert S. ;

Plevritis, Sylvia K. ;

Sachs, Karen ;

Pe'er, Dana ;

Tanner, Scott D. ;

Nolan, Garry P. .

SCIENCE, 2011, 332 (6030) :687-696

[3] Proteomics Quality Control: Quality Control Software for MaxQuant Results [J].

Bielow, Chris ;

Mastrobuoni, Guido ;

Kempa, Stefan .

JOURNAL OF PROTEOME RESEARCH, 2016, 15 (03) :777-787

[4] Ultrasensitive Proteome Profiling for 100 Living Cells by Direct Cell Injection, Online Digestion and Nano-LC-MS/MS Analysis [J].

Chen, Qi ;

Yan, Guoquan ;

Gao, Mingxia ;

Zhang, Xiangmin .

ANALYTICAL CHEMISTRY, 2015, 87 (13) :6674-6680

[5] Simple and Integrated Spintip-Based Technology Applied for Deep Proteome Profiling [J].

Chen, Wendong ;

Wang, Shuai ;

Adhikari, Subash ;

Deng, Zuhui ;

Wang, Lingjue ;

Chen, Lan ;

Ke, Mi ;

Yang, Pengyuan ;

Tian, Ruijun .

ANALYTICAL CHEMISTRY, 2016, 88 (09) :4864-4871

[6] Spatially-Resolved Proteomics: Rapid Quantitative Analysis of Laser Capture Microdissected Alveolar Tissue Samples [J].

Clair, Geremy ;

Piehowski, Paul D. ;

Nicola, Teodora ;

Kitzmiller, Joseph A. ;

Huang, Eric L. ;

Zink, Erika M. ;

Sontag, Ryan L. ;

Orton, Daniel J. ;

Moore, Ronald J. ;

Carson, James P. ;

Smith, Richard D. ;

Whitsett, Jeffrey A. ;

Corley, Richard A. ;

Ambalavanan, Namasivayam ;

Ansong, Charles .

SCIENTIFIC REPORTS, 2016, 6

[7] The importance of using the optimal plasticware and glassware in studies involving peptides [J].

Goebel-Stengel, Miriam ;

Stengel, Andreas ;

Tache, Yvette ;

Reeve, Joseph R., Jr. .

ANALYTICAL BIOCHEMISTRY, 2011, 414 (01) :38-46

[8] SNaPP: Simplified Nanoproteomics Platform for Reproducible Global Proteomic Analysis of Nanogram Protein Quantities [J].

Huang, Eric L. ;

Piehowski, Paul D. ;

Orton, Daniel J. ;

Moore, Ronald J. ;

Qian, Wei-Jun ;

Casey, Cameron P. ;

Sun, Xiaofei ;

Dey, Sudhansu K. ;

Burnum-Johnson, Kristin E. ;

Smith, Richard D. .

ENDOCRINOLOGY, 2016, 157 (03) :1307-1314

[9] Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types [J].

Jaitin, Diego Adhemar ;

Kenigsberg, Ephraim ;

Keren-Shaul, Hadas ;

Elefant, Naama ;

Paul, Franziska ;

Zaretsky, Irina ;

Mildner, Alexander ;

Cohen, Nadav ;

Jung, Steffen ;

Tanay, Amos ;

Amit, Ido .

SCIENCE, 2014, 343 (6172) :776-779

[10] THE ION FUNNEL: THEORY, IMPLEMENTATIONS, AND APPLICATIONS [J].

Kelly, Ryan T. ;

Tolmachev, Aleksey V. ;

Page, Jason S. ;

Tang, Keqi ;

Smith, Richard D. .

MASS SPECTROMETRY REVIEWS, 2010, 29 (02) :294-312

← 1 2 3 4 5 →