Evaluation of ammonium salts as co-matrices for matrix-assisted laser desorption/ionization mass spectrometry of oligonucleotides

✍ Scribed by Y. C. Leo Li; Sau-wan Cheng; T.-W. Dominic Chan

• Publisher: John Wiley and Sons
• Year: 1998
• Tongue: English
• Weight: 156 KB
• Volume: 12
• Category: Article
• ISSN: 0951-4198
• DOI: 10.1002/(sici)1097-0231(19980815)12:15<993::aid-rcm273>3.0.co;2-4

✦ Synopsis

Fourteen ammonium salts have been investigated as co-matrices for negative-ion matrix-assisted laser desorption/ionization (MALDI) analysis of a number of synthetic oligonucleotides in three different matrix systems, including 2,5-dihydroxybenzoic acid, 2-amino-5-nitropyridine (ANP) and 3-hydroxypicolinic acid (HPA). 4-mer, 8-mer and 12-mers of homo-oligodeoxyribonucleotides, including polydeoxyadenosine, polydeoxycytidine, polydeoxyguanosine, polydeoxyinosine, polydeoxythymidine and polyuridine, were used as analytes. Similar to our previous findings (Rapid Commun. Mass Spectrom. 10, 907 (1996)), ammonium fluoride (NH 4 F) and ammonium hydrogen fluoride ((NH 4 )HF 2 ) exhibit the greatest and the most general signal enhancement effects for different oligonucleotides tested. Among the various matrix systems studied, HPA, ANP/NH 4 F and HPA/NH 4 F matrix systems were further evaluated using mixed-base oligonucleotides and longer homo-oligonucleotides. Apart from the signals for the intact molecule-ions, most of the MALDI mass spectra of oligonucleotides show substantial intensities of fragment ions derived presumably from hydrolysis of nucleotide bases (for HPA matrix) and bond cleavage along the phosphodiester linkages (for ANP/NH 4 F matrix). The hydrolysis reaction was tentatively attributed to the presence of acidic additives such as trifluoroacetic acid and, to a lesser extent, from the low pH of the HPA matrices. In conclusion, HPA/NH 4 F shows the best performance in terms of the analysis of high-mass oligonucleotides.