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Application Overview

MALDI-ToF MS (Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry ) is a soft ionization technique that is widely used in the analysis of biomolecules such as proteins, peptides, and oligonucleotides. In MALDI, the sample is mixed with a suitable matrix, and the mixture is spotted on a MALDI plate where the sample and matrix co-crystallize. The spot is irradiated by a laser beam, the matrix absorbs most of the laser energy and transfers it to the analyte molecules. As a result, both matrix and analyte molecules are ejected into the gas phase as ions. This ionization process is illustrated in Figure 1.


The ionized analyte and matrix molecules then enter the mass analyzer where they are sorted/separated according to their mass-to-charge ratio.

The matrix used in MALDI is a conjugated organic compound, usually a weak organic acid, that strongly absorbs UV radiation. Table 1 shows some common matrix compounds and their application for the analysis of specific groups of biomolecules.

Compound Name
α-Cyano-4-hydrocinnamic acid (CHCA) Merck:/Freestyle/LW-Lab-Water/applications/MALDI-ToF/LW-LC-MALDI-Image2-136x65.jpg Peptides <10 kDa
Sinapinic acid (3,5-dimethoxy-4-hydrocinnamic acid), SA Merck:/Freestyle/LW-Lab-Water/applications/MALDI-ToF/LW-LC-MALDI-Image3-136x92.jpg Proteins > 10 kDa
3-Hydropicolinic acid (3-HPA) Merck:/Freestyle/LW-Lab-Water/applications/MALDI-ToF/LW-LC-MALDI-Image4-136x112.jpg Oligonucleotides > 3.5 kDa
2,5-Dihydrobenzoic acid (DHB) Merck:/Freestyle/LW-Lab-Water/applications/MALDI-ToF/LW-LC-MALDI-Image5-136x86.jpg Neutral carbohydrates
Extracted from Principles and Techniques of Biochemistry and Molecular Biology 6th Ed. (Eds K. Wilson and J. Walker, New York: Cambridge University Press, 2005)
Table 1. Examples of common MALDI matrix compounds

Time-of-Flight (ToF) is the most suitable mass analyzer for MALDI, because (1) it has theoretically unlimited mass range, and (2) the pulsed laser in MALDI takes individual 'shots' rather than working in continuous operation. When used in the reflectron mode, ToF measurements can achieve very high resolution.

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