Hello,

Recently stumbled here: http://www.nature.com/articles/srep32272 which may be remotely relevant.

Be it tissue  or individual cells, they all may leach, so why not freeze-dry the entire soup  of preservative/ detergent with bacterial suspension (formaldehyde would be volatile anyways) and extract it all with a suitable solvent that would not extract detergent/ fixative (most solvents would not!). So even though cells are damaged/ permeabilized, they would  be there in that small solution. As a control/ background to subtract, use everything except bacteria in there and compare metabolomics data runs.

Thanks,

 Dear Biswapriya,

thanks a lot for your answer. In my specific case, I would like to flow-sort the fixed and permeabilized bacteria, so I won't anymore have access to the solution they were originally in including the leaked metabolites.