Polyamine co‐matrices for matrix‐assisted laser desorption/Ionization mass spectrometry of oligonucleotides

Abstract

The analysis of oligonucleotides using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has led to the investigation of the use of matrix additives (i.e., co-matrices) to help improve the poor spectral quality commonly observed during the analysis of this class of compounds. The use of certain matrix additives in MALDI-MS has been investigated previously, and these additives have been shown to enhance the desorption/ionization efficiency of oligonucleotides during the MALDI experiment. Specifically, amine bases, such as piperidine, imidazole, and triethylamine, have been shown to improve mass spectral quality as assessed by improved molecular ion resolution and increased molecular ion abundance. These improvements occur due to competition between the oligonucleotide and the co-matrix for protons generated during the MALDI event. Co-matrices with proton affinities near or above the proton affinities of the nucleotide residues serve as proton sinks during the desorption/ionization process. In this work, we have investigated the use of polyamines as co-matrices for MALDI mass spectrometric analysis of oligonucleotides. Spermine tetrahydrochloride, spermine, spermidine trihydrochloride, and spermidine were evaluated for their effectiveness at enhancing the mass spectral quality of oligonucleotides analyzed using MALDI-MS. The solution-phase pK( b) values and the gas-phase proton affinities of these polyamines were determined, and it was found that the polyamines appear to be more basic than the monofunctional amines investigated previously. The mass spectral data shows that spermidine and spermine are extremely effective co-matrices, yielding improved molecular ion resolution and molecular ion abundances. The spermine co-matrices are more effective than the spermidine co-matrices, but adduction problems with the spermine co-matrices limits their overall utility. In general, polyamine co-matrices are found to be more effective than monofunctional amine co-matrices at improving the mass spectral data obtained during MALDI-MS of oligonucleotides.

A survey of useful salt additives in matrix‐assisted laser desorption/ionization mass spectrometry and tandem mass spectrometry of lipids: introducing nitrates for improved analysis

“…Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is relatively well established in small molecule analysis with examples of detection and characterization of lipids, [1][2][3][4][5][6] drugs, [7] carbohydrates, [8] and oligonucleotides. [9,10] The analysis of lipids by MALDI has been a topic of much recent interest and the technique has been used to identify lipid biomarkers in diseases such as Fabry disease, [11] Tay Sachs/Sandhoff, [2] and cancers. [12,13] Both the concentration and the localization of lipids have been implicated in these diseases.…”

“…Lithium and caesium chlorides [35] and silver nitrate [36] have been reported in polymer analysis. Tetraamine spermine [37] and polyamine [10] have been reported in oligonucleotide analysis. Finally, zinc sulphate heptahydrate [38] was reported for the analysis of cyanobacteria.…”

Using sol–gel/crown ether hybrid materials as desalting substrates for matrix‐assisted laser desorption/ionization analysis of oligonucleotides

“…Thus, an ongoing goal in MAL-DI analysis of oligonucleotides is reduction of cation adducts to improve the quality of mass spectra and to lower the detection limits. For example, use of cation-exchange resin beads to remove cations from oligonucleotide solutions, [1][2][3] and addition of a co-matrix during sample preparation, [3][4][5][6][7][8][9][10][11][12][13] have been applied successfully to DNA analysis using MALDI. Comatrices, such as ammonium salts, [6][7][8] triethylamine, 4,5 and the tetraamine spermine, 9,10 have proven to be effective matrix additives for inhibiting the formation of alkali cation adducts.…”

“…The matrices commonly used for oligonucleotide analysis are 3-hydroxypicolinic acid (3-HPA), 6-aza-2-thiothymine (6-ATT), and 2,4,6-trihydroxyacetophenone (2,4,6-THAP). [3][4][5][6][7][8][9][10][11][12][13][14][15] The selection of the matrix and co-matrix is the main determinant of the quality of MALDI mass spectra of oligonucleotides.…”

Fractional Factorial Design of MALDI-TOF-MS Sample Preparations for the Optimized Detection of Phospholipids and Acylglycerols

“…A number of research groups have used matrix additives for the analysis of a variety biological compounds. These additives include the following: ammonium acetate , and citrate for analyzing phosphopeptides and proteins; lithium and cesium chlorides for analyzing polymers; and tetraamine spermine and polyamine for the analysis of oligonucleotides. Interest in using additives has increased due to the quality of MALDI-TOF-MS spectra produced upon their addition. , Hence, this study included the addition of matrix additives to reduce the complexity of MALDI-TOF-MS spectra generated with some of the matrices used in lipid analysis.…”