Development of an efficient, effective, and economical technology for proteome analysis
| Author(s) | Martin, Katherine R. | |
| Author(s) | Le, Ha T. | |
| Author(s) | Abdelgawad, Ahmed | |
| Author(s) | Yang, Canyuan | |
| Author(s) | Lu, Guotao | |
| Author(s) | Keffer, Jessica L. | |
| Author(s) | Zhang, Xiaohui | |
| Author(s) | Zhuang, Zhihao | |
| Author(s) | Asare-Okai, Papa Nii | |
| Author(s) | Chan, Clara S. | |
| Author(s) | Batish, Mona | |
| Author(s) | Yu, Yanbao | |
| Date Accessioned | 2024-07-03T19:40:56Z | |
| Date Available | 2024-07-03T19:40:56Z | |
| Publication Date | 2024-06-11 | |
| Description | This article was originally published in Cell Reports: Methods. The version of record is available at: https://doi.org/10.1016/j.crmeth.2024.100796. © 2024 The Authors. Published by Elsevier Inc. Creative Commons Attribution (CC BY 4.0) http://creativecommons.org/licenses/by/4.0/ | |
| Abstract | Highlights • Rapid, robust, and cost-effective alternative to proteomics sample preparation • Versatile filter devices can meet a wide range of proteomics analysis needs • On-filter in-cell digestion facilitates low-input proteomics • Ready-to-go E3 and E4 filter devices are available Motivation Conventional proteomics sample processing methods often have high technical barriers to broad biomedical scientists, leading to difficulties for quick adoption and standardization. Existing protocols are also typically associated with costly reagents and accessories, making them less feasible for resource-limited settings as well as for clinical proteomics and/or core facilities where large numbers of samples are usually processed. Thus, there is a strong unmet need for an easy-to-use, reliable, and low-cost approach for general proteomics sample preparation. Summary We present an efficient, effective, and economical approach, named E3technology, for proteomics sample preparation. By immobilizing silica microparticles into the polytetrafluoroethylene matrix, we develop a robust membrane medium, which could serve as a reliable platform to generate proteomics-friendly samples in a rapid and low-cost fashion. We benchmark its performance using different formats and demonstrate them with a variety of sample types of varied complexity, quantity, and volume. Our data suggest that E3technology provides proteome-wide identification and quantitation performance equivalent or superior to many existing methods. We further propose an enhanced single-vessel approach, named E4technology, which performs on-filter in-cell digestion with minimal sample loss and high sensitivity, enabling low-input and low-cell proteomics. Lastly, we utilized the above technologies to investigate RNA-binding proteins and profile the intact bacterial cell proteome. Graphical abstract available at: https://doi.org/10.1016/j.crmeth.2024.100796 | |
| Sponsor | We gratefully acknowledge support from the National Institute of General Medical Sciences (NIGMS) under award number P20GM104316 for the MS instrument, the National Science Foundation (NSF) under award number 2242127 (M.B.), NSF BIO-1817651 (C.S.C.), and NIH R01GM129468 (Z.Z.). We would like to thank Zaining Yun in the Chemical & Biomolecular Engineering Department for providing the Jurkat cells. We also thank Dr. Yong Zhao in the W.M. Keck Center for the microscopy analysis. The graphical abstract was created with BioRender. Author contributions K.R.M., H.T.L., and C.Y. performed some of the preparation for the method evaluation experiments; A.A. and M.B. designed the RNA probes, performed CARPID and AP experiments, and interpreted data; J.L.K. and C.S.C. performed the ES-1 cell culture experiments and interpreted the transcriptomic data; G.L. and X.Z. assisted with manufacturing of GB membranes and guided the design of the E3 and E4 filters; Z.Z. and P.N.A.-O. assisted with the cell experiments and oversaw data collection and analysis; and Y.Y. conceived the study, collected data for patent application, performed the majority of sample preparations, analyzed data, and wrote the manuscript with input from all other authors. All authors provided feedback and edited the manuscript. Declaration of interests G.L. and X.Z. are employees of CDS Analytical LLC. Y.Y. is a paid consultant of CDS Analytical LLC. Y.Y. is a named inventor on a patent application (PCT/US2023/020215) for the technologies developed in this study. The patent was published under the publication number WO2023/212205 and has been licensed exclusively to CDS Analytical LLC through the University of Delaware. | |
| Citation | Martin, Katherine R., Ha T. Le, Ahmed Abdelgawad, Canyuan Yang, Guotao Lu, Jessica L. Keffer, Xiaohui Zhang, et al. “Development of an Efficient, Effective, and Economical Technology for Proteome Analysis.” Cell Reports Methods 4, no. 6 (June 2024): 100796. https://doi.org/10.1016/j.crmeth.2024.100796. | |
| ISSN | 2667-2375 | |
| URL | https://udspace.udel.edu/handle/19716/34559 | |
| Language | en_US | |
| Publisher | Cell Reports: Methods | |
| dc.rights | Attribution 4.0 International | en |
| dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | |
| Keywords | proteomics | |
| Keywords | sample preparation | |
| Keywords | Empore membrane | |
| Keywords | E3technology | |
| Keywords | E4technology | |
| Keywords | on-filter digestion | |
| Keywords | in-cell digestion | |
| Keywords | glass beads | |
| Keywords | silica microparticles | |
| Title | Development of an efficient, effective, and economical technology for proteome analysis | |
| Type | Article |
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