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. High CMC detergents may be removed by dialysis, but commonly used detergents like triton X-100 can only be removed by special techniques. Remember, the ideal sample contains nothing but peptides!
You may want to try substituting an acid hydrolzable detergent in your protocol. There are also commercial detergent removal kits that we have seen success with. Ask us for details.
The protocol supplied at the following link is generally useful for removing a variety of small molecule contaminants, although not many detergents.
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.