My whole lysate proteins were prepared in 8M Urea buffer +2M Thio-Urea+ 4% CHAPS. In preparation for LC-MS/MS analysis, the samples need to undergo desalting and be switched to Ammonium bicarbonate (AmBic) before introduction into the column. I'm curious whether there are alternative economical LC compatible precipitation techniques available that don't require a desalting kit. Alternatively, could the samples be sonicated directly with AmBic before proceeding with in-solution digestion?
For many samples, basic membrane dialysis provides for an inexpensive way to remove buffer salts. We often us dialysis to remove low molecular weight substances or salts from our protein/peptide samples BEFORE starting HPLC or LC-MS analysis.
If you need a solution other than dialysis, FASP would be the most convenient approach to perform buffer exchange. Since 8M urea and CHAPS composition is present in your lysis buffer, protein solubility is high and it is not easy to precipitate the targets. Therefore precipitation approaches cannot be recommended unless you perform buffer exchange to get rid of detergent and urea components. By implementing FASP or S-Trap you can perform on membrane cleavage (in solution digest) which occurs at Ambic environment. Alternatively, you may run your sample through PAGE and perform in-gel digestion, this also removes the buffer components. Your lysate buffer is highly denaturant (conveniently). Therefore, if you remove the solubility agents and precipitate them (TCA for instance), you will need similar solubility agents for resuspension, Ambic alone would not be efficient to solubilize proteins.
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