My group and I have some samples of frozen mouse brains that are fixed in paraformaldehyde. However, tissue quality does not allow us to perform the immunofluorescence protocol. So, so that we don't lose these samples, we are looking for a way to quantify some proteins through western blotting. But we don't know if there is a way to perform this technique in a brain fixed with paraformaldehyde.
The fixed brain tissue samples are not usually used for other proteomic analysis as the fixation process is thought to make brain tissue unsuitable. The protein extraction from formaldehyde-fixed tissues is hampered by the Schiff base formation between the amino groups of proteins and formaldehyde.
However, advances in antigen-retrieval procedures have allowed detectable levels of protein to be solubilized from formaldehyde fixed tissue, opening the door for aldehyde-fixed samples to be used for proteomic approaches.
Recently by Thacker et al. (2021) developed a new method for the use on fixed-brain lysates to make them suitable for analysis by Western blot.
Jonathan S. Thacker, Delaney Andersen, Stanley Liang, Natalia Zieniewicz, Juan S. Trivino-Paredes, Patrick C. Nahirney, Brian R. Christie, Unlocking the brain: A new method for Western blot protein detection from fixed brain tissue, Journal of Neuroscience Methods, Volume 348, 2021, 108995, ISSN 0165-0270,
https://doi.org/10.1016/j.jneumeth.2020.108995.
Good luck
Another possibility : When you have sections of this mice brains you can run a immuno with biotinylated secondary antibodies , ABC or StrepAvidin-POX and DAB staining. Use the free floating method, that increases the intensity of the signal. Afterwards you can analyse the protein-expression desitometrically.
Advantage of this method: you will not get only the information waether the protein would be expressed, you will get also the information where exactly it would be expressed. The ABC-DAB-Method makes the analysis easier because you can distiguish the protein signal form unspesific backgroundstaining in a better way.
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