1 IITB-Monash Research Academy , Mumbai, India .
2 Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay , Mumbai, India .
OMICS. 2017 Nov;21(11):678-683. doi: 10.1089/omi.2017.0128. Epub 2017 Oct 12.
Proteomics is a crucial postgenomic biotechnology for functional and systems scale analyses in cell and integrative biology, not to mention clinical and precision medicine research. However, a fundamental requirement for an accurate examination of the protein complement of cells is an efficient method for extracting the proteins. This study reports on the evaluation of three protein extraction methods: trichloroacetic acid (TCA)-acetone, phenol, and TRIzol, in the eustigmatophyte alga Microchloropsis gaditana CCMP526 for proteomic analysis. M. gaditana is a potential candidate for algal-based biofuels. This industrially important strain is also rich in dietary oil and pigments and is used as feed in the aquaculture industry. Liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based proteomic analysis was performed for proteins obtained using the three extraction methods and their effects were examined by the abundance ratio. Protein yield was higher using the TCA-acetone and phenol methods than with the TRIzol method. The TCA method was superior than other methods examined here in terms of protein coverage and abundance. Subcellular localization of the identified proteins revealed no significant difference among the extraction methods. Importantly, each method revealed a unique set of proteins. To the best of our knowledge, this is the first report on evaluation of protein extraction methods for the proteomic analysis of M. gaditana CCMP526. These observations underscore the importance of using multiple protein extraction methods for comprehensive proteome coverage, as the field of proteomics edges toward diverse applications in biofuels, aquaculture industry, marine biology, and agriculture.
蛋白质组学是一种至关重要的后基因组生物技术，可用于细胞和综合生物学的功能和系统规模分析，更不用说临床和精准医学研究了。然而，准确检查细胞蛋白质组成的一个基本要求是提取蛋白质的有效方法。本研究报告了三种蛋白质提取方法在等鞭藻藻类微绿球藻 CCMP526 中的评价：三氯乙酸（TCA）-丙酮、酚和 TRIzol，用于蛋白质组学分析。M. gaditana 是藻类生物燃料的潜在候选者。这种工业上重要的菌株富含食用油脂和色素，并且在水产养殖行业中用作饲料。使用三种提取方法获得的蛋白质进行基于液相色谱-串联质谱（LC-MS/MS）的蛋白质组学分析，并通过丰度比检查其效果。使用 TCA-丙酮和酚方法获得的蛋白质产量高于 TRIzol 方法。TCA 方法在蛋白质覆盖率和丰度方面优于本文中检查的其他方法。鉴定出的蛋白质的亚细胞定位在提取方法之间没有明显差异。重要的是，每种方法都揭示了一组独特的蛋白质。据我们所知，这是首次报道用于微绿球藻 CCMP526 蛋白质组学分析的蛋白质提取方法的评估。这些观察结果强调了使用多种蛋白质提取方法进行全面蛋白质组覆盖的重要性，因为蛋白质组学领域逐渐应用于生物燃料、水产养殖行业、海洋生物学和农业等领域。
