Before I go for LC-MS i wish to do initial check and have a view of probable metabolites which would help me in getting better result.
All metabolites are common within crops under abiotic stress.e.g proline content.
Thank You K. Singh. But there are some metabolites which are specific to particular crops and to specific regions of the plant.
It depends on what you mean for initial checks and the answer is not so simple as one can expect. Obviously, as first thing, you should read a lot of manuscripts on rice metabolome and rice metabolic changes due to abiotic stress, in order to have a clear “state of art” in your mind. If the abiotic stress results in visible effects, you should choose the stress parameters that are strong enough to show symptoms without causing the death of the plant. In this way, you can “visually” compare the normal state of the plant with the altered one. Then, you should focus on the methods to extract and analyse primary and specialized (secondary) metabolites. For my personal experience, secondary metabolites are strongly affected by biotic and abiotic stresses. For instance, PAL (phenylalanine ammonia-lyase) genes are triggered by heat, UV and other stressors, causing the synthesis and accumulation of secondary metabolites including phenylpropanoids and flavonoids. Therefore, I suggest you to start with these metabolites and you could perform HPLC-DAD or the easiest spectrophotometric analysis at 280, 320 and 350 nm to detect and compare the content of phenolic compounds. Then you can move on LC-MS. In my opinion, it is important to set up an appropriate experimental design rather than focusing on which metabolites can give you the best results, since untargeted metabolomics aims to detect as many metabolite as possible without any previous information.
All the best
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