To study the milk protein synthesis in the cells I culture primary bovine mammary cells on top of a Matrigel layer in a transwell system, so my cell yield is not very high and also the cells are not embedded in the Matrigel layer. After hormone treatment period, I plan to wash the cell layer in ice-cold PBS and then scrape and centrifuge in cold PBS, remove the liquid snap freeze and preserve the pellet for the upcoming proteomic analysis of relevant milk proteins (LC-MSMS). Can I know if this is going to be enough to get rid of the matrix, so it does not interfere with the following lysis step, after thawing?
I came across the below publication where Cell Recovery Solution is used for this purpose with 1 hour incubation on ice. I'm not sure if that's necessary for my case because this work is on organoids embedded in the matrix. Also because I don't have a high cell yield I'd like to avoid repeated washing steps. And with an hour incubation step, shouldn't I worry about protein degradation?
https://www.nature.com/articles/s41598-018-29837-1
Many thanks in advance.
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