What buffer should I use for MALDI Mass Spectrometry analysis of my protein sample?
In general, MALDI-MS is more tolerant to contamination than other MS methods. However, the salts and detergents that are commonly used in biomolecular science can still interfere. Either with crystallisation or ionisation or both. Therefore particular attention should be paid to sample purification and storage solvents. Do not utilise buffers, salts or detergents such as SDS [1, 2].
It is best to remove buffer salts and detergents (e.g. by dialysis) prior to analysis. You should also dissolve the sample in a suitable solvent (e.g. 0.1% TFA/water) which will not degrade the spectrum. If there is too much salt in a sample the salt signal intensity becomes very large. As a result, it suppresses the sample signal, thus giving no sample spectrum. In cases where it is not possible to remove these contaminants, the sample should be in a higher concentration. It may then be possible to dilute the sample to the point where the contaminants will have little effect on the spectrum .
One would normally like to have any sample in a volatile buffer without salts and detergents. Examples of volatile buffers are ammonium acetate, acetonitrile, ammonium formate, TFA (trifluoroacetic acid), or formic acid in water [1-3].
Buffers not compatible with MALDI-MS analysis of proteins thus include:
Buffer components that will not work with Mass Spec analysis include:
- Tween 80
- Tween 20
- Triton X
- Sodium Azide
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 Börnsen, K.O.: “Influence of Salts, Buffers, Detergents, Solvents, and Matrices on MALDI-MS Protein Analysis in Complex Mixtures“, Mass Spectrometry of Proteins and Peptides, 2000
 Hillenkamp et al: “Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers“, Analytical Chemistry, 1991
 Dave et al: “Preparation and Analysis of Proteins and Peptides Using MALDI TOF/TOF Mass Spectrometry“, Current Protocols in Protein Science, 2011