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, drugs, carbohydrates, and oligonucleotides . 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, Tay Sachs/Sandhoff, and cancers .…”

A study of noncovalent complexes involving single-stranded DNA and polybasic compounds using nanospray mass spectrometry

“…The only observations of natural polyamineoligonucleotide complexes by mass spectrometry have been reported in the case where spermine was used as matrix additives for oligonucleotide analysis by MALDI-TOF [12][13][14][15]. In this case, protonated sites of the polyamine were expected to bond DNA phosphate in solution to displace alkaline cations [12][13][14] and stabilize duplexes [15]. Ideally, polyamine protons were transferred to DNA phosphates during sample crystallization or desorption/ ionization process and the oligonucleotide free of alkaline cation and polyamine was observed.…”

Solid-phase fluorescence and ionization efficiency in negative-ion matrix-assisted laser desorption/ionization of neutral oligosaccharides: Interaction between β-carboline matrix and ammonium salt

“…Pieles et al [21] showed that the addition of diammonium hydrogen citrate to a trihydroxyacetophenone matrix is an effective combination for reducing cation adducts and improving ion production of the oligodeoxynucleotides. Limbach et al [22][23][24] examined organic base co-matrices such as triethylamine, imidazole, piperidine, and polyamine. It was thought that these additives reduced the cation adduction problem and improved the gas-phase stability of the oligodeoxynucleotides.…”