Metabolite extraction is considered as one of the most important for quality controlling steps in metabolomic research. In the present study, optimal extraction protocol for fungal intracellular metabolites was investigated. Two extraction protocols with different solvent systems, methanol extraction and biphasic extraction under different pH conditions were compared. Number of detected peaks, sample-to-sample variation, and throughput of whole process were taken into account as criteria. Extracted metabolites were analyzed by gas chromatography-mass spectrometry (GC-MS) and principal component analysis (PCA). The extraction protocol using methanol as extraction solvent provided the highest number of detected peaks (~ 300 peaks) with the ease and speed, suggesting that the methanol-extraction method was suitable for intracellular metabolites extraction from P. chrysosporium. However, depending on the nature of metabolites of interest, the biphasic extraction method under different pH conditions is suitable for a targeted analysis.
