An improved method for sensitive quantification of isoprenoid diphosphates in the astaxanthin-accumulating Haematococcus pluvialis

•The first use of Tissue Lyser for extraction of metabolites in H. pluvialis cells.•The most sensitive UHPLC-MS-MS method for determination of isoprenoid diphosphates.•The first discovery of cisoid isomers of FPP and GGPP in H. pluvialis. A sensitive method has been established to simultaneously determine the concentrations of isopentenyl pyrophosphate (IPP), geranyl diphosphate (GPP), farnesyl diphosphate (FPP) and geranylgeranyl diphosphate (GGPP) in H. pluvialis under different environments. This method increased the extraction efficiency of isoprenoid diphosphates through releasing isoprenoid diphosphates using Tissue Lyser. This is the first report on the efficient extraction method of metabolites in H. pluvialis cells, being suitable for all algae and plants with thick cell wall. The concentrations of isoprenoid diphosphates were measured on poroshell EC-C18 column by UHPLC-MS/MS with the LODs of 0.015, 0.027, 0.022 and 0.076 pmol for DMAPP, GPP, FPP and GGPP, respectively. It is the most sensitive method for the determination of isoprenoid diphosphates in any sample to date. Using this method, the profile of isoprenoid diphosphates was analyzed and cisoid isomers of FPP and GGPP, (Z, Z)-FPP and (Z, Z, Z-GGPP) were found firstly in H. pluvialis.