I washed cell pellets thrice with 1XPBS, centrifuged at 500g for 4-5 min and removed PBS to store at -80c. Unfortunately, protein count was low after Urea cell lysis. We expected more protein than what we got after lysis. 

So, there might be several reasons for this low protein quantity. The centrifuge was not perfect meaning that PBS supernatant contained a lot of cell after separating from cell pellets or cell disrupted while centrifuging. Now I am looking for a standard protocol for washing cell pellets without disrupting cell/losing any cell in the washing buffer.  

If anybody has a better idea to share with me that would be great. Thanks.

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