Matrix nucleic acid analysis

FAB and PD have been replaced by electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) in the analytical mass spectrometry laboratory, because both of these newer techniques have a wider mass range of analysis and have lower detection limits. ESI and MALDI have become invaluable ionization techniques for nonvolatile components. This is particularly true for a wide range of biological molecules including proteins, peptides, nucleic acids, etc. Samples can be analyzed by ESI using either direct injection or introduction through liquid chromatography. 

The most widely used mass spectrometric identification procedure is MALDI-Tof analysis of the entire peptide mixture. Gas-phase matrix interaction with peptide ions in MALDI-Tof results in singly charged ions, giving a mass profile that is highly characteristic of the protein from which the peptides are derived. These peptide masses (actually protonated peptide molecular ions, MH+) can be used to search databases (either protein or nucleic acid databases) to identify the proteins. The two most important factors in successfully identifying proteins by this approach are the number of matching peptide masses and the accuracy of the peptide mass determination. 

Ono T, Scalf M, Smith LM. 2 -Fluoro modified nucleic acids polymerase-directed synthesis, properties and stability to analysis by matrix-assisted laser desorption/ionizationmass spectrometry. Nucleic Acids Res 1997 25 4581-4588. 

A large number of variants of gel electrophoresis are used in bioanalytical analysis to allow separation and characterization of biomolecules, in particular nucleic acids (DNA, RNA) and proteins. The term gel refers to the matrix used to separate biomolecules, and in most cases is a cross-linked polymer. 

If free amino acids are to be analyzed in foods or feeds, it is advisable to remove matrix components such as lipids, carbohydrates, and nucleic acids from the sample. Of course, the necessary extraction steps are time-consuming, but higher concentrations of such compounds may severely interfere with the amino acid analysis. After hydrolysis of protein-free mixtures of nucleosides, nucleotides, and nucleic acids, Paddock et al. [38] even observed the formation of amino acids, predominantly glycine. 

Maizel, J. V., Lenk, R. P. (1981) Enhanced graphic matrix analysis of nucleic acid and protein sequences, Proc. Natl. Acad, Sci. USA 78 7665-7669. 

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