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

Nature Communications

Volumn 9, Issue 1, 2018, Pages

  Zhu, Ying ^a   Piehowski, Paul D ^b   Zhao, Rui ^a   Chen, Jing ^c   Shen, Yufeng ^b   Moore, Ronald J ^b   Shukla, Anil K ^b   Petyuk, Vladislav A ^b   Campbell Thompson, Martha ^c   Mathews, Clayton E ^c   Smith, Richard D ^b   Qian, Wei Jun ^b   Kelly, Ryan T ^a  

^a PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^b PACIFIC NORTHWEST NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF FLORIDA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BETA 2 MICROGLOBULIN; GLUCAGON; INSULIN; PROTEOME; PROTEIN;

ALGORITHM; CELL; DOWNSCALING; IDENTIFICATION METHOD; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; NANOPARTICLE; NANOTECHNOLOGY; PROTEIN; PROTEOMICS;

ADSORPTION; ARTICLE; CELL COUNT; CELL HETEROGENEITY; CELL LYSATE; CONTROLLED STUDY; EVAPORATION; GENE ONTOLOGY; HELA CELL LINE; HUMAN; HUMAN CELL; HUMAN TISSUE; INSULIN DEPENDENT DIABETES MELLITUS; INTRACELLULAR SPACE; LIQUID CHROMATOGRAPHY-MASS SPECTROMETRY; MAMMAL CELL; PANCREAS ISLET ALPHA CELL; PH; PHENOTYPE; PROTEIN ANALYSIS; PROTEOMICS; CHEMISTRY; GENE EXPRESSION PROFILING; GENETICS; MASS SPECTROMETRY; METABOLISM; PANCREAS ISLET;

MAMMALIA;

GENE EXPRESSION PROFILING; HUMANS; ISLETS OF LANGERHANS; MASS SPECTROMETRY; PROTEINS; PROTEOME; PROTEOMICS;

EID: 85042804880     PISSN: None     EISSN: 20411723     Source Type: Journal    
DOI: 10.1038/s41467-018-03367-w     Document Type: Article

References (44)

1. Achim, K. et al. High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin. Nat. Biotechnol. 33, 503-509 (2015).
2. Jaitin, D. A. et al. Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types. Science 343, 776-779 (2014).
3. Shapiro, E., Biezuner, T. & Linnarsson, S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet. 14, 618-630 (2013).
4. Bendall, S. C. et al. Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum. Science 332, 687-696 (2011).
5. Smith, R. D., Shen, Y. & Tang, K. Ultrasensitive and quantitative analyses from combined separations-mass spectrometry for the characterization of proteomes. Acc. Chem. Res. 37, 269-278 (2004).
6. Shen, Y. et al. Ultrasensitive proteomics using high-efficiency on-line micro-SPE-NanoLC-NanoESI MS and MS/MS. Anal. Chem. 76, 144-154 (2004).
7. Sun, L. et al. Ultrasensitive and fast bottom-up analysis of femtogram amounts of complex proteome digests. Angew. Chem. Ed. 52, 13661-13664 (2013).
8. Kelly, R. T., Tolmachev, A. V., Page, J. S., Tang, K. & Smith, R. D. The ion funnel: theory, implementations, and applications. Mass. Spectrom. Rev. 29, 294-312 (2010).
9. Li, S. et al. An integrated platform for isolation, processing, and mass spectrometry-based proteomic profiling of rare cells in whole blood. Mol. Cell. Proteom. 14, 1672-1683 (2015).
10. Sun, X., Kelly, R. T., Tang, K. & Smith, R. D. Ultrasensitive nanoelectrospray ionization-mass spectrometry using poly(dimethylsiloxane) microchips with monolithically integrated emitters. Analyst 135, 2296-2302 (2010).
11. Wang, H. et al. Development and evaluation of a micro-and nanoscale proteomic sample preparation method. J. Proteome Res. 4, 2397-2403 (2005).
12. Wiśniewski, J. R., Ostasiewicz, P. & Mann, M. High recovery FASP applied to the proteomic analysis of microdissected formalin fixed paraffin embedded cancer tissues retrieves known colon cancer markers. J. Proteome Res. 10, 3040-3049 (2011).
13. Chen, Q., Yan, G., Gao, M. & Zhang, X. Ultrasensitive proteome profiling for 100 living cells by direct cell injection, online digestion and nano-LC-MS/MS aalysis. Anal. Chem. 87, 6674-6680 (2015).
14. Chen, W. et al. Simple and integrated Spintip-based technology applied for deep proteome profiling. Anal. Chem. 88, 4864-4871 (2016).
15. Waanders, L. F. et al. Quantitative proteomic analysis of single pancreatic islets. Proc. Natl. Acad. Sci. USA 106, 18902-18907 (2009).
16. Huang, E. L. et al. Snapp: simplified nanoproteomics platform for reproducible global proteomic analysis of nanogram protein quantities. Endocrinology 157, 1307-1314 (2016).
17. Wang, N., Xu, M., Wang, P. & Li, L. Development of mass spectrometry-based shotgun method for proteome analysis of 500 to 5000 cancer cells. Anal. Chem. 82, 2262-2271 (2010).
18. Lombard-Banek, C., Moody, S. A. & Nemes, P. Single-cell mass spectrometry for discovery proteomics: quantifying translational cell heterogeneity in the 16-cell frog (Xenopus) embryo. Angew. Chem. Ed. 55, 2454-2458 (2016).
19. Sun, L. et al. Single cell proteomics using frog (Xenopus laevis) blastomeres isolated from early stage embryos, which form a geometric progression in protein content. Anal. Chem. 88, 6653-6657 (2016).
20. Wiśniewski, J. R., Hein, M. Y., Cox, J. & Mann, M. A 'Proteomic Ruler' for protein copy number and concentration estimation without spike-in standards. Mol. Cell. Proteom. 13, 3497-3506 (2014).
21. Goebel-Stengel, M., Stengel, A., Taché, Y. & Reeve, J. R. The importance of using the optimal plasticware and glassware in studies involving peptides. Anal. Biochem. 414, 38-46 (2011).
22. Zhu, Y., Zhang, Y. X., Cai, L. F. & Fang, Q. Sequential operation droplet array: an automated microfluidic platform for picoliter-scale liquid handling, analysis, and screening. Anal. Chem. 85, 6723-6731 (2013).
23. Vandermarliere, E., Mueller, M. & Martens, L. Getting intimate with trypsin, the leading protease in proteomics. Mass. Spectrom. Rev. 32, 453-465 (2013).
24. Shen, Y. et al. Coupling to 15-150-μm-i. d. column liquid chromatography for proteomic analysis. Anal. Chem. 75, 3596-3605 (2003).
25. Tyanova, S., Temu, T. & Cox, J. The MaxQuant computational platform for mass spectrometry-based shotgun proteomics. Nat. Protoc. 11, 2301-2319 (2016).
26. Bielow, C., Mastrobuoni, G. & Kempa, S. Proteomics quality control: Quality Control Software for MaxQuant results. J. Proteome Res. 15, 777-787 (2016).
27. 18O-labeled universal reference sample. J. Proteome Res. 8, 290-299 (2009).
28. Volpe, P. & Eremenko-Volpe, T. Quantitative studies on cell proteins in suspension cultures. Eur. J. Biochem. 12, 195-200 (1970).
29. Zeiler, M., Straube, W. L., Lundberg, E., Uhlen, M. & Mann, M. A Protein Epitope Signature Tag (PrEST) Library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines. Mol. Cell. Proteom. 11, O111.009613 (2012).
30. Clair, G. et al. Spatially-resolved proteomics: rapid quantitative analysis of laser capture microdissected alveolar tissue samples. Sci. Rep. 6, 39223 (2016).
31. Pisania, A. et al. Quantitative analysis of cell composition and purity of human pancreatic islet preparations. Lab. Invest. 90, 1661-1675 (2010).
32. Rodriguez-Calvo, T. et al. Heterogeneity and lobularity of pancreatic pathology in type 1 diabetes during the prediabetic phase. J. Histochem. Cytochem. 63, 626-636 (2015).
33. Richardson, S. J. et al. Islet cell hyperexpression of HLA class I antigens: a defining feature in type 1 diabetes. Diabetologia 59, 2448-2458 (2016).
34. Rowe, P. A., Campbell-Thompson, M. L., Schatz, D. A. & Atkinson, M. A. The pancreas in human type 1 diabetes. Semin. Immunopathol. 33, 29-43 (2011).
35. White, A. K. et al. High-throughput microfluidic single-cell RT-qPCR. Proc. Natl. Acad. Sci. USA 108, 13999-14004 (2011).
36. Zhu, Y. & Fang, Q. Integrated droplet analysis system with electrospray ionization-mass spectrometry using a hydrophilic tongue-based droplet extraction interface. Anal. Chem. 82, 8361-8366 (2010).
37. Zhu, Y. et al. Printing 2-dimentional droplet array for single-cell reverse transcription quantitative PCR assay with a microfluidic robot. Sci. Rep. 5, 9551 (2015).
38. Zhu, Y. et al. Nanoliter-scale protein crystallization and screening with a microfluidic droplet robot. Sci. Rep. 4, 5046 (2014).
39. Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671-675 (2012).
40. Yu, Y. Q., Gilar, M., Lee, P. J., Bouvier, E. S. P. & Gebler, J. C. Enzyme-friendly, mass spectrometry-compatible surfactant for in-solution enzymatic digestion of proteins. Anal. Chem. 75, 6023-6028 (2003).
41. Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731-740 (2016).
42. Spitzer, M., Wildenhain, J., Rappsilber, J. & Tyers, M. BoxPlotR: a web tool for generation of box plots. Nat. Methods 11, 121-122 (2014).
43. Zhang, B. et al. Detecting differential and correlated protein expression in label-free shotgun proteomics. J. Proteome Res. 5, 2909-2918 (2006).
44. Vizcaíno, J. A. et al. 2016 update of the PRIDE database and its related tools. Nucleic Acids Res. 44, D447-D456 (2016).