Reducing the alkali cation adductions of oligonucleotides using sol-gel-assisted laser desorptionionization mass spectrometry

Abstract

The alkali cation adductions of oligonucleotides dramatically degrade MALDI mass spectra and even affect the detection limit. Desalting is generally involved in MALDI sample preparation. This work demonstrates the feasibility of using 3,4-diaminobenzoic acid (DABA) and 3,5-DABA as the MALDI matrix for oligonucleotide analysis. Furthermore, sodium ion adducts of oligonucleotides were simultaneously reduced in the mass spectra when DABA was used as the MALDI matrix and sol-gel material was used as the sample support. However, depositing the sample on the sample support was very difficult, and the lack of homogeneity of analytes/matrix distribution on the sample support also led the analyte signals to be revealed only in "sweet spots". Alternatively, DABA was doped into sol-gel materials to generate homogeneous DABA/sol-gel hybrid film. The DABA/sol-gel hybrid film was used as the sample substrate to assist the desorption/ionization of analytes. The analyte signals were evenly found on the sample substrate. The sodium ion adductions of oligonucleotides were also effectively suppressed. The sample preparation used in this approach resembles that used in the authors' previous study, involving sol-gel-assisted laser desorption/ionization (SGALDI) mass spectrometry (Lin, Y.-S.; Chen, Y.-C. Anal. Chem. 2002, 74, 5793-5798.) The SGALDI approach was demonstrated to be effective in assisting the desorption/ionization of peptides and small proteins. Herein, the SGALDI material, DABA/sol-gel hybrid material, was successfully applied to oligonucleotide analysis, and good-quality mass spectra were obtained without extra desalting. Additionally, the presence of 0.1% SDS in the oligonucleotide sample solution was tolerated without degrading the mass spectra. The largest detectable molecular size for oligonucleotides was 72 mer. The detection limit for 24 mer of oligonucleotide was 20 fmol.