Display options
Cite
Aballo TJ, Roberts DS, Melby JA, et al. Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. J Proteome Res. 2021;20(8):4203-4211doi: 10.1021/acs.jproteome.1c00446.
Aballo, T. J., Roberts, D. S., Melby, J. A., Buck, K. M., Brown, K. A., & Ge, Y. (2021). Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. Journal of proteome research, 20(8), 4203-4211. https://doi.org/10.1021/acs.jproteome.1c00446
Aballo, Timothy J, et al. "Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro." Journal of proteome research vol. 20,8 (2021): 4203-4211. doi: https://doi.org/10.1021/acs.jproteome.1c00446
Aballo TJ, Roberts DS, Melby JA, Buck KM, Brown KA, Ge Y. Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro. J Proteome Res. 2021 Aug 06;20(8):4203-4211. doi: 10.1021/acs.jproteome.1c00446. Epub 2021 Jul 08. PMID: 34236868; PMCID: PMC8349881.
Copy Download .nbib Format: NLM
Share it on

J Proteome Res. 2021 Aug 06;20(8):4203-4211. doi: 10.1021/acs.jproteome.1c00446. Epub 2021 Jul 08.

Ultrafast and Reproducible Proteomics from Small Amounts of Heart Tissue Enabled by Azo and timsTOF Pro.

Journal of proteome research

Timothy J Aballo, David S Roberts, Jake A Melby, Kevin M Buck, Kyle A Brown, Ying Ge

Affiliations

  1. Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.
  2. Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.
  3. Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
  4. Department of Surgery, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States.
  5. Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States.

PMID: 34236868 PMCID: PMC8349881 DOI: 10.1021/acs.jproteome.1c00446

Abstract

Global bottom-up mass spectrometry (MS)-based proteomics is widely used for protein identification and quantification to achieve a comprehensive understanding of the composition, structure, and function of the proteome. However, traditional sample preparation methods are time-consuming, typically including overnight tryptic digestion, extensive sample cleanup to remove MS-incompatible surfactants, and offline sample fractionation to reduce proteome complexity prior to online liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. Thus, there is a need for a fast, robust, and reproducible method for protein identification and quantification from complex proteomes. Herein, we developed an ultrafast bottom-up proteomics method enabled by Azo, a photocleavable, MS-compatible surfactant that effectively solubilizes proteins and promotes rapid tryptic digestion, combined with the Bruker timsTOF Pro, which enables deeper proteome coverage through trapped ion mobility spectrometry (TIMS) and parallel accumulation-serial fragmentation (PASEF) of peptides. We applied this method to analyze the complex human cardiac proteome and identified nearly 4000 protein groups from as little as 1 mg of human heart tissue in a single one-dimensional LC-TIMS-MS/MS run with high reproducibility. Overall, we anticipate this ultrafast, robust, and reproducible bottom-up method empowered by both Azo and the timsTOF Pro will be generally applicable and greatly accelerate the throughput of large-scale quantitative proteomic studies. Raw data are available via the MassIVE repository with identifier MSV000087476.

Keywords: bottom-up proteomics; human heart proteomics; photocleavable surfactant; quantitative proteomics; sample preparation

References

  1. BMC Genomics. 2008 Oct 16;9:488 - PubMed
  2. Protein Sci. 1994 Nov;3(11):1975-83 - PubMed
  3. Proteomics. 2017 Jan;17(1-2): - PubMed
  4. Mol Cell Proteomics. 2018 Dec;17(12):2534-2545 - PubMed
  5. Anal Chim Acta. 2021 Apr 29;1156:338349 - PubMed
  6. Mol Cell Proteomics. 2020 Jun;19(6):1058-1069 - PubMed
  7. Oncotarget. 2017 Jul 18;8(29):48321-48332 - PubMed
  8. Nat Commun. 2017 Nov 13;8(1):1469 - PubMed
  9. Nat Methods. 2009 May;6(5):359-62 - PubMed
  10. J Sep Sci. 2005 Sep;28(14):1694-703 - PubMed
  11. J Cell Physiol. 2019 Aug;234(8):13720-13734 - PubMed
  12. Nat Methods. 2019 May;16(5):417-420 - PubMed
  13. J Proteome Res. 2014 Dec 5;13(12):6176-86 - PubMed
  14. Anal Chem. 2014 Feb 4;86(3):1551-9 - PubMed
  15. J Chromatogr B Analyt Technol Biomed Life Sci. 2005 Mar 5;817(1):35-47 - PubMed
  16. Annu Rev Anal Chem (Palo Alto Calif). 2016 Jun 12;9(1):449-72 - PubMed
  17. Cell Syst. 2017 Jun 28;4(6):587-599.e4 - PubMed
  18. Angew Chem Int Ed Engl. 2020 May 25;59(22):8406-8410 - PubMed
  19. Chem Rev. 2007 Aug;107(8):3687-714 - PubMed
  20. Proteomics. 2014 May;14(9):1006-0 - PubMed
  21. Anal Chem. 2001 Dec 1;73(23):5683-90 - PubMed
  22. Mol Cell Proteomics. 2017 Apr;16(4):694-705 - PubMed
  23. J Proteome Res. 2015 Dec 4;14(12):5378-87 - PubMed
  24. Anal Methods. 2013 Sep 21;5(18): - PubMed
  25. Nat Biotechnol. 2008 Dec;26(12):1367-72 - PubMed
  26. J Proteome Res. 2018 Jul 6;17(7):2480-2490 - PubMed
  27. Mol Cell Proteomics. 2020 Jul;19(7):1132-1144 - PubMed
  28. J Proteome Res. 2011 Apr 1;10(4):1794-805 - PubMed
  29. Nat Methods. 2016 Sep;13(9):731-40 - PubMed
  30. Nature. 2016 Sep 14;537(7620):347-55 - PubMed
  31. Chem Rev. 2007 Aug;107(8):3654-86 - PubMed
  32. Nature. 2014 May 29;509(7502):575-81 - PubMed
  33. PLoS Biol. 2021 Apr 19;19(4):e3001144 - PubMed
  34. Anal Chem. 2020 Dec 15;92(24):15693-15698 - PubMed
  35. Chem Rev. 2013 Apr 10;113(4):2343-94 - PubMed
  36. J Clin Invest. 2014 Apr;124(4):1734-44 - PubMed

Substances

MeSH terms

Publication Types

Grant support