Table 1.

Comparison of methods for assessing subcellular metabolomics

Parameter	Aqueous organelles	Non-aqueous chloroplasts	Non-aqueous fractionation
Purity of fractions	(Often) very high	High	Low
Leakage	Leakage of compounds with active transport and breakage	No leakage of hydrophilic compounds, low leakage of lipophilic compounds	No leakage of hydrophilic compounds, low leakage of lipophilic compounds
Continuation of metabolism	Yes	No	No
Contamination correction	Not needed	Preferred	Fundamental to method
Accuracy	High for stable compounds, low for metabolites with high turnover and efflux transporters	High for compounds absent from the vacuole	Iterative solution, approximation
Advantages	Proper determination of stable compounds	Proper estimate of chloroplast levels	Estimates metabolite levels in various compartments
Disadvantages	Instability of organelles, duration of preparation	Little definition of extra-chloroplast levels	Simplified assumption of uniform distribution of marker enzymes