New Mass-Spectrometry-Compatible Degradable Surfactant for Tissue Proteomics
Open accessAbstract
Tissue proteomics is increasingly recognized for its role in biomarker discovery and disease mechanism investigation. However, protein solubility remains a significant challenge in mass spectrometry (MS)-based tissue proteomics. Conventional surfactants such as sodium dodecyl sulfate (SDS), the preferred surfactant for protein solubilization, are not compatible with MS. Herein, we have screened a library of surfactant-like compounds and discovered an MS-compatible degradable surfactant (MaSDeS) for tissue proteomics that solubilizes all categories of proteins with performance comparable to SDS. The use of MaSDeS in the tissue extraction significantly improves the total number of protein identifications from commonly used tissues, including tissue from the heart, liver, and lung. Notably, MaSDeS significantly enriches membrane proteins, which are often under-represented in proteomics studies. The acid degradable nature of MaSDeS makes it amenable for high-throughput MS-based proteomics. In addition, the thermostability of MaSDeS allows for its use in experiments requiring high temperature to facilitate protein extraction and solubilization. Furthermore, we have shown that MaSDeS outperforms the other MS-compatible surfactants in terms of overall protein solubility and the total number of identified proteins in tissue proteomics. Thus, the use of MaSDeS will greatly advance tissue proteomics and realize its potential in basic biomedical and clinical research. MaSDeS could be utilized in a variety of proteomics studies as well as general biochemical and biological experiments that employ surfactants for protein solubilization.
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Acid-cleavable surfactants Rapigest, ProteaseMAX, and MaSDeS were developed as MS-compatible surfactants for digestion and MS analysis.
“Previously, acid-cleavable surfactants such as Rapigest [28], ProteaseMAX [29], and MS-compatible degradable surfactant MaSDeS [30] were developed as MS-compatible surfactants to enable protein solubilization for digestion and MS-analysis.”
From Top-down proteomics: challenges, innovations, and applications in basic and clinical research (2020) · cites this paper as [30]
Acid-labile surfactants have been effective for bottom-up proteomics, but none have shown direct compatibility with intact protein MS for top-down proteomics.
“Efforts have been made in developing various acid-labile surfactants which have been effective for bottom-up proteomics10–13, however none have demonstrated direct compatibility with intact protein MS for top-down proteomics.”
From A photocleavable surfactant for top-down proteomics (2019) · cites this paper as [10]
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Cites
Krogh, A., Larsson, B., von Heijne, G., & Sonnhammer, E. L. L. (2001) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.4315 · Cited by 12,654 · see citing works
Universal sample preparation method for proteome analysis
Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352 · see citing works
Cardiac excitation–contraction coupling
Bers, D., & Despa, S. (2002) · Nature · doi:10.1038/415198a · Cited by 4,927 · see citing works
STRING v9.1: protein-protein interaction networks, with increased coverage and integration
Franceschini, A., Szklarczyk, D., Frankild, S., Kuhn, M., Simonovic, M., Roth, A., Lin, J., Minguez, P., Bork, P., von Mering, C., et al. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks1094 · Cited by 4,398 · see citing works
How many drug targets are there?
Overington, J. P., Al-Lazikani, B., & Hopkins, A. L. (2006) · Nature Reviews Drug Discovery · doi:10.1038/nrd2199 · Cited by 3,505 · see citing works
A draft map of the human proteome
Kim, M.-S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., et al. (2014) · Nature · doi:10.1038/nature13302 · Cited by 2,198 · see citing works
Crystal structure of the human β2 adrenergic G-protein-coupled receptor
Rasmussen, S. G. F., Choi, H., Rosenbaum, D. M., Kobilka, T. S., Thian, F. S., Edwards, P. C., Burghammer, M. C., Ratnala, V. R. P., Sanishvili, R., Fischetti, R. F., et al. (2007) · Nature · doi:10.1038/nature06325 · Cited by 1,935 · see citing works
Role of integrins in cell invasion and migration
Hood, J. D., & Cheresh, D. A. (2002) · Nature reviews. Cancer · doi:10.1038/nrc727 · Cited by 1,781 · see citing works
Cell adhesion and signalling by cadherins and Ig-CAMs in cancer
Cavallaro, U., & Christofori, G. (2004) · Nature reviews. Cancer · doi:10.1038/nrc1276 · Cited by 1,314 · see citing works
Evaluation of methods for the prediction of membrane spanning regions
Möller, S., Croning, M. D. R., & Apweiler, R. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.7.646 · Cited by 1,214 · see citing works
Phospholamban: a crucial regulator of cardiac contractility
MacLennan, D. H., & Kranias, E. G. (2003) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1151 · Cited by 1,088 · see citing works
Extraction, purification and analysis of histones
Shechter, D., Dormann, H. L., Allis, C. D., & Hake, S. B. (2007) · Nature Protocols · doi:10.1038/nprot.2007.202 · Cited by 1,054 · see citing works
Toll‐like Receptor and RIG‐1‐like Receptor Signaling
Kawai, T., & Akira, S. (2008) · Annals of the New York Academy of Sciences · doi:10.1196/annals.1443.020 · Cited by 985 · see citing works
Kußmaul, L., & Hirst, J. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0510977103 · Cited by 720 · see citing works
Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis
Masuda, T., Tomita, M., & Ishihama, Y. (2008) · Journal of Proteome Research · doi:10.1021/pr700658q · Cited by 655 · see citing works
A method for the comprehensive proteomic analysis of membrane proteins
Wu, C. C., MacCoss, M. J., Howell, K. E., & Yates, J. R. (2003) · Nature Biotechnology · doi:10.1038/nbt819 · Cited by 651 · see citing works
The application of mass spectrometry to membrane proteomics
Wu, C. C., & Yates, J. R. (2003) · Nature Biotechnology · doi:10.1038/nbt0303-262 · Cited by 558 · see citing works
Mass spectrometry of intact membrane protein complexes
Laganowsky, A., Reading, E., Hopper, J. T. S., & Robinson, C. V. (2013) · Nature Protocols · doi:10.1038/nprot.2013.024 · Cited by 409 · see citing works
Sample preparation and digestion for proteomic analyses using spin filters
Manza, L. L., Stamer, S. L., Ham, A. L., Codreanu, S. G., & Liebler, D. C. (2005) · PROTEOMICS · doi:10.1002/pmic.200401063 · Cited by 383 · see citing works
Structure, dynamics and function of nuclear pore complexes
D’Angelo, M. A., & Hetzer, M. W. (2008) · Trends in Cell Biology · doi:10.1016/j.tcb.2008.07.009 · Cited by 377 · see citing works
Aquaporin water channels in mammals
Ishibashi, K., Hara, S., & Kondo, S. (2008) · Clinical and Experimental Nephrology · doi:10.1007/s10157-008-0118-6 · Cited by 366 · see citing works
Micelles Protect Membrane Complexes from Solution to Vacuum
Barrera, N. P., Bartolo, N. D. D., Booth, P. J., & Robinson, C. V. (2008) · Science · doi:10.1126/science.1159292 · Cited by 362 · see citing works
Proteomics of Integral Membrane ProteinsTheory and Application
Speers, A. E., & Wu, C. C. (2007) · Chemical Reviews · doi:10.1021/cr068286z · Cited by 325 · see citing works
Yu, Y.-Q., Gilar, M., Lee, P. J., Bouvier, E. S. P., & Gebler, J. C. (2003) · Analytical Chemistry · doi:10.1021/ac0346196 · Cited by 313 · see citing works
Membrane proteins and membrane proteomics
Tan, S., Tan, H. T., & Chung, M. C. M. (2008) · PROTEOMICS · doi:10.1002/pmic.200800597 · Cited by 291 · see citing works
Zhou, M., Morgner, N., Barrera, N. P., Politis, A., Isaacson, S. C., Matak‐Vinković, D., Murata, T., Bernal, R. A., Stock, D., & Robinson, C. V. (2011) · Science · doi:10.1126/science.1210148 · Cited by 268 · see citing works
Pervasive combinatorial modification of histone H3 in human cells
Garcia, B. A., Pesavento, J. J., Mizzen, C. A., & Kelleher, N. L. (2007) · Nature Methods · doi:10.1038/nmeth1052 · Cited by 242 · see citing works
Optimization of Mass Spectrometry-Compatible Surfactants for Shotgun Proteomics
Chen, E. I., Cociorva, D., Norris, J. L., & Yates, J. R. (2007) · Journal of Proteome Research · doi:10.1021/pr060682a · Cited by 218 · see citing works
Top‐down proteomics in health and disease: Challenges and opportunities
Gregorich, Z. R., & Ge, Y. (2014) · PROTEOMICS · doi:10.1002/pmic.201300432 · Cited by 217 · see citing works
Self-citationMembrane proteins and membrane proteomics
Shi-you, Y. (2009) · Zhongguo linchuang yaolixue yu zhiliaoxue · Cited by 203 · see citing works
Zhang, J., Guy, M. J., Norman, H. S., Chen, Y.-C., Xu, Q., Dong, X., Guner, H., Wang, S., Kohmoto, T., Young, K. H., et al. (2011) · Journal of Proteome Research · doi:10.1021/pr200258m · Cited by 194 · see citing works
Self-citationSurfactant effects on protein structure examined by electrospray ionization mass spectrometry
Loo, R. R. O., Dales, N., & Andrews, P. C. (1994) · Protein Science · doi:10.1002/pro.5560031109 · Cited by 184 · see citing works
Top-Down and Bottom-Up Proteomics of SDS-Containing Solutions Following Mass-Based Separation
Botelho, D. M., Wall, M. J., Vieira, D. B., Fitzsimmons, S., Liu, F., & Doucette, A. A. (2010) · Journal of Proteome Research · doi:10.1021/pr900949p · Cited by 170 · see citing works
Advances in the Mass Spectrometry of Membrane Proteins: From Individual Proteins to Intact Complexes
Barrera, N. P., & Robinson, C. V. (2011) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-062309-093307 · Cited by 154 · see citing works
Rapid and Deep Human Proteome Analysis by Single-dimension Shotgun Proteomics
Pirmoradian, M., Budamgunta, H., Chingin, K., Zhang, B., Astorga-Wells, J., & Zubarev, R. A. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o113.028787 · Cited by 144 · see citing works
Hellberg, P., Bergström, K., & Holmberg, K. (2000) · Journal of Surfactants and Detergents · doi:10.1007/s11743-000-0118-z · Cited by 144 · see citing works
Structure, Function, and Modification of the Voltage Sensor in Voltage-Gated Ion Channels
Liin, S. I., & Elinder, F. (2008) · Cell Biochemistry and Biophysics · doi:10.1007/s12013-008-9032-5 · Cited by 141 · see citing works
Duan, X., Young, R. F., Straubinger, R. M., Page, B. J., Cao, J., Wang, H., Yu, H., Canty, J. M., & Qu, J. (2009) · Journal of Proteome Research · doi:10.1021/pr900001t · Cited by 125 · see citing works
Whitelegge, J. P., le Coutre, J., Lee, J. C., et al. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.19.10695 · Cited by 116 · see citing works
Peng, Y., Gregorich, Z. R., Valeja, S. G., Zhang, H., Cai, W., Chen, Y.-C., Guner, H., Chen, A. J., Schwahn, D. J., Hacker, T. A., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.040675 · Cited by 107 · see citing works
Self-citationAugmented Phosphorylation of Cardiac Troponin I in Hypertensive Heart Failure
Dong, X., Sumandea, C. A., Chen, Y.-C., Garcia-Cazarin, M. L., Zhang, J., Balke, C. W., Sumandea, M. P., & Ge, Y. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m111.293258 · Cited by 99 · see citing works
Self-citationIntegral Membrane Proteins and Bilayer Proteomics
Whitelegge, J. P. (2013) · Analytical Chemistry · doi:10.1021/ac303064a · Cited by 93 · see citing works
Doucette, A. A., Craft, D., & Li, L. (2000) · Analytical Chemistry · doi:10.1021/ac000176j · Cited by 84 · see citing works
Chen, E. I., McClatchy, D. B., Park, S. K., & Yates, J. (2008) · Analytical Chemistry · doi:10.1021/ac800606w · Cited by 78 · see citing works
Quantitative proteomics in resected renal cancer tissue for biomarker discovery and profiling
Atrih, A., Mudaliar, M., Zakikhani, P., Lamont, D. J., Huang, J. T.-J., Bray, S. E., Barton, G. J., Fleming, S., & Nabi, G. (2014) · British Journal of Cancer · doi:10.1038/bjc.2014.24 · Cited by 71 · see citing works
CUNHA, S., & MOHLER, P. (2006) · Cardiovascular Research · doi:10.1016/j.cardiores.2006.03.018 · Cited by 65 · see citing works
Altered Proteome Biology of Cardiac Mitochondria Under Stress Conditions
Zhang, J., Liem, D. A., Mueller, M., Wang, Y., Zong, C., Deng, N., Vondriska, T. M., Kôrge, P., Drews, O., MacLellan, W. R., et al. (2008) · Journal of Proteome Research · doi:10.1021/pr070371f · Cited by 64 · see citing works
Self-citationMass Spectrometry Compatible Surfactant for Optimized In-Gel Protein Digestion
Saveliev, S. V., Woodroofe, C. C., Sabat, G., Adams, C. M., Klaubert, D., Wood, K., & Urh, M. (2013) · Analytical Chemistry · doi:10.1021/ac302423t · Cited by 62 · see citing works
Lin, S., Wein, S. P., Gonzales-Cope, M., Otte, G. L., Yuan, Z., Afjehi‐Sadat, L., Maile, T. M., Berger, S. L., Rush, A. J., Lill, J. R., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o113.036459 · Cited by 62 · see citing works
Comparison between procedures using SDS for shotgun proteomic analyses of complex samples
Bereman, M. S., Egertson, J. D., & MacCoss, M. J. (2011) · PROTEOMICS · doi:10.1002/pmic.201100045 · Cited by 60 · see citing works
Identification of membrane proteins by tandem mass spectrometry of protein ions
Carroll, J., Altman, M. C., Fearnley, I., & Walker, J. (2007) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.0706817104 · Cited by 60 · see citing works
Ion-current-based Proteomic Profiling of the Retina in a Rat Model of Smith-Lemli-Opitz Syndrome
Tu, C., Li, J., Jiang, X.-S., Sheflin, L. G., Pfeffer, B. A., Behringer, M. D., Fliesler, S. J., & Qu, J. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.027847 · Cited by 54 · see citing works
A Targeted Quantitative Proteomics Strategy for Global Kinome Profiling of Cancer Cells and Tissues
Xiao, Y., Guo, L., & Wang, Y. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.036905 · Cited by 53 · see citing works
Nomura, E., Katsuta, K., Ueda, T., et al. (2004) · Journal of Mass Spectrometry · doi:10.1002/jms.578 · Cited by 47 · see citing works
Wu, F., Sun, D., Wang, N., Gong, Y., & Li, L. (2011) · Analytica Chimica Acta · doi:10.1016/j.aca.2011.04.039 · Cited by 44 · see citing works
Carberry, S., Zweyer, M., Swandulla, D., & Ohlendieck, K. (2013) · Analytical Biochemistry · doi:10.1016/j.ab.2013.08.004 · Cited by 37 · see citing works
Qu, J., Young, R. F., Page, B. J., Shen, X., Tata, N., Li, J., Duan, X., Fallavollita, J. A., & Canty, J. M. (2014) · Journal of Proteome Research · doi:10.1021/pr5000472 · Cited by 21 · see citing works
Deal, C. D., & Kaplan, S. (1983) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)32443-8 · Cited by 15 · see citing works
Collins, J. W., Coldham, N. G., Salguero, F. J., et al. (2010) · Applied and Environmental Microbiology · doi:10.1128/aem.03115-09 · Cited by 15 · see citing works
Tissue Proteomics and Metabolomics: An Excellent Start and a Promising Future
Veenstra, T. D., & Zhou, M. (2009) · Journal of Proteome Research · doi:10.1021/pr900157d · Cited by 11 · see citing works
Method for Protein Subfractionation of Cardiovascular Tissues Before DIGE Analysis
Didangelos, A., Yin, X., & Mayr, M. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-573-2_20 · Cited by 11 · see citing works
Zhou, J., Huang, S., Bi, D., et al. (2009) · Electrophoresis · doi:10.1002/elps.200900391 · Cited by 10 · see citing works
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- Authors
- Chang, Y.-H., Gregorich, Z. R., Chen, A. J., Hwang, L., Guner, H., Yu, D., Zhang, J., & Ge, Y.
- Affiliations
- University of Wisconsin System (US)
- University of Minnesota (US)
- Corresponding author
- Ge, Ying
- Venue
- Journal of Proteome Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2015-01-30
- Volume
- 14
- Issue
- 3
- Pages
- 1587-1599
- ISSN
- 1535-3893 (ISSN-L)
- 1535-3907
- PMC
- PMC4384424
- OpenAlex
- W2321496253
- Cited by
- 80
- References
- 62
- Citations by year
- 2026: 1 · 2025: 3 · 2024: 10 · 2023: 12 · 2022: 5 · 2021: 7 · 2020: 11 · 2019: 8 · 2018: 7 · 2017: 6 · 2016: 7 · 2015: 3
- FWCI
- 3.42
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of Proteome Research (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Heart, Lung, and Blood Institute (HL109810, R01 HL096971, R01 HL114120)
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Physical Sciences › Chemistry › Spectroscopy › Mass Spectrometry Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- tissue proteomics, protein solubilization, sodium dodecyl sulfate, membrane protein enrichment, tissue extraction, protein identification
- MeSH terms
- Animals, Mass Spectrometry, Surface-Active Agents, Swine, Proteomics
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