Buffers for MALDI mass spectrometry analysis of a protein

Apr 28. 2016


What buffer should I use for MALDI analysis?

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 [3].

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:

  • TRIS
  • PBS

Buffer components that will not work with Mass Spec analysis include:

  • Tween 80
  • Tween 20
  • Triton X
  • Glycerol
  • DMSO
  • SDS
  • Sodium Azide

Learn more about our protein analysis and characterization services >>>


[1]          Börnsen, K.O.: “Influence of Salts, Buffers, Detergents, Solvents, and Matrices on MALDI-MS Protein Analysis in Complex Mixtures“, Mass Spectrometry of Proteins and Peptides2000

[2]          Hillenkamp et al: Matrix-assisted laser desorption/ionization mass spectrometry of biopolymers“, Analytical Chemistry1991

[3]          Dave et al: Preparation and Analysis of Proteins and Peptides Using MALDI TOF/TOF Mass Spectrometry“, Current Protocols in Protein Science, 2011

More posts about MW Analysis of Intact Proteins
  • Buffers for MALDI mass spectrometry analysis of a protein

About Alphalyse

Alphalyse uses expertise in the field of protein chemistry and bioinformatics, combined with top-of-the-line mass spectrometry equipment, to provide protein analysis services globally.

Alphalyse aims to deliver high quality data and customer service to all of our clients in a fast and convenient way.


Newsletter Subscribe to The Alphalyse Newsletter and get more
information on protein analysis methods and applications
© 2021 Alphalyse, Inc.