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URL: https://dx.doi.org/DOI:10.17504/protocols.io.434gyqw

Authors: Benjamin Lau, Abrizah Othman

Summary: Protein solubility is a critical prerequisite to any proteomics analysis. Combination of urea/thiourea and 3-[(3-cholamidopropyl)dimethylammonio]-1-propanesulfonate (CHAPS) have been routinely used to enhance protein solubilization for oil palm proteomics studies in recent years. The goals of these proteomics analysis are essentially to complement the knowledge regarding the regulation networks and mechanisms of the oil palm fatty acid biosynthesis. Through omics integration, the information is able to build a regulatory model to support efforts in improving the economic value and sustainability of palm oil in the global oil and vegetable market. Our study evaluated the utilization of sodium deoxycholate as an alternative solubilization buffer/additive to urea/thiourea and CHAPS. Efficiency of urea/thiourea/CHAPS, urea/CHAPS, urea/sodium deoxycholate and sodium deoxycholate buffers in solubilizing the oil palm (Elaeis guineensis var. Tenera) mesocarp proteins were compared. Based on the protein yields and electrophoretic profile, combination of urea/thiourea/CHAPS were shown to remain a better solubilization buffer and additive, but the differences with sodium deoxycholate buffer was not significant. Furthermore, a deeper mass spectrometric and statistical analyses on the identified proteins and peptides from all the evaluated solubilization buffers revealed that sodium deoxycholate had similar efficiency in solubilizing proteins from oil palm mesocarps. However, it was worth to note that observed limitations to the application of sodium deoxycholate in protein solubilization were the interference with protein quantitation and only 70% of the total identified proteins were shared between the buffers. The former limitation could be rectified through a 4-fold dilution but further works are needed to determine the importance of the remaining 30% unique proteins. All the proteomics data are available via ProteomeXchange with identifier PXD013255. In conclusion, sodium deoxycholate is applicable in the solubilization of proteins extracted from oil palm mesocarps to an efficiency level comparable to that of urea/thiourea/CHAPS buffer.

Associated Publications: Lau BYC, Othman A (2019) Evaluation of sodium deoxycholate as solubilization buffer for oil palm proteomics analysis. PLoS ONE 14(8): e0221052. doi: 10.1371/journal.pone.0221052

Affiliations: Malaysian Palm Oil Board, Malaysian Palm Oil Board

External URL: https://doi.org/10.1371/journal.pone.0221052

Version: 2

Publication Date: 2019

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