In-gel Digestion - Extraction

Extraction

After finishing the digestion the peptides generated in this process have to be extracted from the gel matrix. This is accomplished by one or several extraction steps. The gel particles are incubated with an extraction solution and the supernatant is collected. In the first extraction, almost all of the peptide is recovered, the repetition of the extraction step can increase the yield of the whole process by only 5-10%. To meet the requirements of peptides with different physical and chemical properties an iterative extraction with basic or acidic solutions is performed. For the extraction of acidic peptides a solution similar to the concentration and composition of the digestion buffer is used; basic peptides are extracted in dependence to the intended mass spectrometric method with a low concentrated acidic solution of formic acid for ESI and trifluoroacetic acid for MALDI respectively. Studies on model proteins showed a recovery of approximately 70–80% of the expected peptide yield by extraction from the gel. Many protocols contain an additional fraction of acetonitrile to the extraction solution which, in concentrations above 30% (v/v), is effective in reducing the adsorption of peptides to the surface of reaction tubes and pipette tips. The liquid of the pooled extracts is evaporated in a centrifugal evaporator. If the volatile salt ammonium bicarbonate was used for the basic extraction, it is partially removed in the drying process. The dried peptides can be stored at -20°C for at least six months.