Investigation on the stability in plant metabolomics with a special focus on freeze-thaw cycles: LC–MS and NMR analysis to Cassiae Semen (Cassia obtusifolia L.) seeds as a case study

Metabolomics is a rapid and sensitive tool for the detection of dynamic metabolic compositions in the study of systemic metabolic consequences. However, it is also susceptible to a tiny variation of pre-analytical handling procedures. To provide reproducible results, specific knowledge on metabolites perturbance along with different freeze-thaw cycles (FTCs) is needed for further metabolomics studies. In this paper, five FTCs of germinated Cassiae Semen (CS) were chosen as a case study to investigate the influence of FTC effect based on UHPLC-Q-Orbitrap-MS and NMR technologies. A total of 108 metabolites were relatively quantified by LC–MS and NMR analyses. Principal component analysis (PCA) showed that the first and second FTC samples are welly separated from the other groups; however, the extent of FTC-induced effects are smaller after the third cycle. Upon five consecutive FTCs, alterations which consisted of decreased stachyose, sucrose, norrubrofusarin-6-O-β-d-glucopyranoside, and quercetin 3-(3″-acetylgalactoside), as well as increased phenylalanine, leucine, isoleucine, methionine, phenylalanine, mannose, gluconic acid, and valine, could be observed. FTC does not exert the same effect on all metabolites. Although a large number of secondary metabolites were stable when subjected to five FTCs, FTC effects may lead to false-positive in the discovery of biomarker. In the case of reusing plant seed samples, no more than three consecutive freeze-thaw cycles were found advisable. This work provides unique perspectives on the FTC effects, which may fill in some existing gaps in the knowledge of the stability of plant metabolites during sample pre-handling.