Issue 11, 2023

All-in-One digital microfluidics pipeline for proteomic sample preparation and analysis

Abstract

Highly sensitive and reproducible analysis of samples containing low amounts of protein is restricted by sample loss and the introduction of contaminants during processing. Here, we report an All-in-One digital microfluidic (DMF) pipeline for proteomic sample reduction, alkylation, digestion, isotopic labeling and analysis. The system features end-to-end automation, with integrated thermal control for digestion, optimized droplet additives for sample manipulation and analysis, and an automated interface to liquid chromatography with tandem mass spectrometry (HPLC-MS/MS). Dimethyl labeling was integrated into the pipeline to allow for relative quantification of the trace samples at the nanogram level, and the new pipeline was applied to evaluating cancer cell lines and cancer tissue samples. Several known proteins (including HSP90AB1, HSPB1, LDHA, ENO1, PGK1, KRT18, and AKR1C2) and pathways were observed between model breast cancer cell lines related to hormone response, cell metabolism, and cell morphology. Furthermore, differentially quantified proteins (such as PGS2, UGDH, ASPN, LUM, COEA1, and PRELP) were found in comparisons of healthy and cancer breast tissues, suggesting potential utility of the All-in-One pipeline for the emerging application of proteomic cancer sub-typing. In sum, the All-in-One pipeline represents a powerful new tool for automated proteome processing and analysis, with the potential to be useful for evaluating mass-limited samples for a wide range of applications.

Graphical abstract: All-in-One digital microfluidics pipeline for proteomic sample preparation and analysis

Supplementary files

Article information

Article type
Edge Article
Submitted
01 Feb 2023
Accepted
07 Feb 2023
First published
22 Feb 2023
This article is Open Access

All publication charges for this article have been paid for by the Royal Society of Chemistry
Creative Commons BY license

Chem. Sci., 2023,14, 2887-2900

All-in-One digital microfluidics pipeline for proteomic sample preparation and analysis

J. Peng, C. Chan, S. Zhang, A. A. Sklavounos, M. E. Olson, E. Y. Scott, Y. Hu, V. Rajesh, B. B. Li, M. D. Chamberlain, S. Zhang, H. Peng and A. R. Wheeler, Chem. Sci., 2023, 14, 2887 DOI: 10.1039/D3SC00560G

This article is licensed under a Creative Commons Attribution 3.0 Unported Licence. You can use material from this article in other publications without requesting further permissions from the RSC, provided that the correct acknowledgement is given.

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