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The electrospray ionization method we use requires that the sample be free from salts and from substances such as detergents that suppress ionization.
Many affinity tag procedures and kits have detergents in their buffers! If you can't avoid detergents in your elution buffers, they must be removed prior to enzymatic digestion of the sample. Remember, the ideal sample contains nothing but peptides!
The protocol supplied at the following link is generally useful for removing a variety of small molecule contaminants.
TCA precipitation of proteins
Another common problem is the introduction into the sample of contaminants that leach out of plastics. Pay close attention to solvent compatibilities of tubes and pipets you use during sample preparation. For example, do not pipet concentrated acid with plastic pipet tips. |
