Time for multiple protein extraction methods in proteomics?

Proteomics has become a valuable tool for investigating many aspects of cell and organismal biology. 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 the evaluation of three protein extraction methods; TCA-Acetone, phenol, and TRIzol, on Microchloropsis gaditana CCMP526 for proteomic analysis. LC-MS/MS based proteomic analysis was performed for proteins obtained using the different methods and the effect of the different extraction methods was examined by abundance ratio. Sub-cellular localization of the identified proteins revealed no significant difference between the extraction methods. Protein yield was higher using the TCA-Acetone and phenol methods than with the TRIzol method. A comparative analysis of three extraction methods revealed that the TCA method was superior in terms of protein coverage and abundance. Further, it was interesting to note that each method revealed a unique set of proteins, reinstating the importance of using multiple protein extraction methods for comprehensive proteome coverage.