There are many methods to extract proteins form human tissues out there. The majority of them use an extraction buffer containing variable concentrations of detergents and protease inhibitors to preserve the extracted proteins as much as possible and keep them functional until being analyzed by downstream applications, like western blot, ELISA, etc. One drawback of this chemical extraction is the interaction of the buffer components with antigen-antibody binding in the analysis. The interaction is sometimes difficult to predict, therefore, validation of the sample matrix is necessary before going into the real analysis, e.g., for ELISA, spike-and-recovery, linearity-of-dilution are two known validation assays to this effect. For more info about these two assay you may find this answer useful. One optimal way would be to avoid such interaction by avoiding the use of extraction buffer altogether and using mechanical methods plus protease inhibitors, instead. I don't know the drawback of this method, but one may be it is not as effective to get cytokines out their vesicles to be accessible by assay analysis.
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