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The matrix-assisted laser desorption/ionization (MALDI) method has been used with an external ion source Fourier transform mass spectrometer (FIMS) to analyze single-stranded, mixed-base oligomers of DNA. It is demonstrated that ultrahigh mass resolution (830 000 fwhm) can be achieved for small oligomers, and high resolution (136 000 fwhm) can be achieved for a 25-mer at m/z 7634. MALDI-FTMS can clearly separate the molecular ion peaks from analyte-matrix adduct peaks and alkali metal-containing species that result from replacement of hydrogen ions with sodium or potassium ions at multiple sites along the phosphate backbone. Previous MALDI-FTMS studies of oligonucleotides had two limitations: (1) low sensitivity due to difficulty in trapping the high kinetic energy ions made by the laser and (2) fragmentation of the ions due to the long delay (tens to hundreds of milliseconds) between their formation and detection. Both of these problems are alleviated in the present study. With the external ion source FTMS instrument, ions made by MALDI are injected at low energy into the analyzer cell by a rf-only quadrupole ion guide, captured by gating the voltage on the trapping plates, and cooled by a 0.5-s pulse of argon gas. Under these conditions, fragmentation is minimized, and DNA ions can be trapped in the FTMS analyzer cell for greater than 50 s. Sensitivity is also improved, as demonstrated by detection of 1 pmol of a single-stranded, mixed-base 20-mer of DNA, with a signal-to-noise ratio greater than 20:1.

A new calibration method has been developed for Fourier transform mass spectrometry (FTMS) that is accurate to better than 0.001% (10 ppm) for peptides and proteins up to 5700 Da. The custom-designed FTMS instrument used for this work has a matrix-assisted laser desorption/ionization (MALDI) source located outside of the magnetic field in a differentially pumped chamber, and ions are injected through the fringing fields of the magnet into the FTMS analyzer cell by a long quadrupole ion guide. The mass spectrometer is calibrated with four model compounds ([Arg8]-vasopressin, melittin, bovine insulin B-chain, and bovine insulin) of known molecular mass. The set of measured ion resonance frequencies (f) for these compounds are fit to a three-term calibration equation of the form f = A(z/m) + B(V) + C(V2) (m/z), where m/z is the mass-to-charge ratio of a calibrant peak, V is the trapping voltage, and A, B, and C are calibration coefficients that depend on the magnetic field strength and the dimensions of the analyzer cell. The same set of calibration coefficients can be used for many weeks because the magnet and the electronics of the FTMS instrument are very stable. This method is useful because unknowns can be run separately without the need to add an internal calibration compound in with the sample.