MATRIX-ASSISTED LASER-DESORPTION IONIZATION FOURIER-TRANSFORM MASS-SPECTROMETRY OF OLIGODEOXYRIBONUCLEOTIDES

Conditions for the matrix-assisted laser desorption/ionization (MALDI) of oligodeoxyribonucleotides at 355 nm, developed using a 3-Tesla Fou rier-transform ion cyclotron resonance mass spectrometer (FTMS), are r eported. Efficient ion trapping and matrix selection are critical to t he desorption and detection of oligonucleotides by FTMS. The achievabl e upper mass limit for the MALDI-FTMS of biomolecules on our 3-Tesla s ystem has been extended from approximately 2 kDa to 6 kDa through the use of pulsed-trapping-plate ion deceleration techniques. By implement ing the deceleration techniques, molecular ions for bovine insulin (MW = 5733.5), an oligodeoxythymidylic acid, pd[T]10 (MW = 3060.0), and a mixed-base 12-mer (MW = 3611.5) have been measured. For the analysis of oligonucleotides by FTMS, selection of an appropriate MALDI matrix is essential for the generation of [M-H]- ions. 3-Hydroxypicolinic aci d provides a significant improvement over 2,5-dihydroxybenzoic acid fo r production of deprotonated molecules particularly for mixed-base oli gomers. MALDI studies using FTMS have been duplicated using a newly co nstructed time-of-flight mass spectrometer (TOFMS) and oligonucleotide fragmentation on the TOFMS is reduced relative to that observed by FT MS. This may be a consequence of the longer times (milliseconds) requi red for FTMS detection.