Preparation of Samples for Mass Spectroscopy

1. Dialyze samples exhaustively against 20 mM ammonium bicarbonate. As much sodium as possible must be removed.
2. Use a fresh 1mL Sepak column for each sample. Load with a SLOW flow rate as follows:
1. 10mL 100% acetonitrile.
2. 10mL dH2O.
3. 5mL 20 mM ammonium bicarbonate.
4. Sample.
5. 5mL 20 mM ammonium bicarbonate.
6. 5mL dH2O.
7. 3 mL 10% acetonitrile.
8. 3mL 70% acetonitrile.
3. Save the 10% acetonitrile elution in a separate tube.
4. The 70% acetonitrile elution should contain you protein. Split this between 2 centrifuge tubes and dry in the speed vac on the medium setting with the radiant cover.
5. Picomolar concentrations are enough for MALDI. Typically they will take a concentration estimate at the analysis center and make serial dilutions.