MALDI on a Chip: Analysis of Arrays of Low-Femtomole to Subfemtomole Quantities of Synthetic Oligonucleotides and DNA Diagnostic Products Dispensed by a Piezoelectric Pipet

A piezoelectric pipet is used to dispense arrays of low-nanoliter aliquots of matrix and DNA into individual etched wells on <1 in.² silicon chips prior to their semiautomated analysis by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Spectrum acquisition is expedited relative to conventional "large-spot" MALDI since the resulting miniaturized samples are approximately the same size as the irradiation area of the ionization/desorption laser; thus, searching for crystal regions from which intense analyte signals may be obtained is not necessary. Using a linear TOF instrument designed for scanning high-density arrays of samples, mass spectra from as little as 0.2 fmol (45 nM) of a 36-mer DNA have been acquired from single miniature elements. Spot-to-spot reproducibility from microdispensed samples is superior to that using conventional pipets; in less than 6 min, spectra with high signal-to-noise ratios were acquired from 100 elements containing 8 fmol of a 25-mer. Low-nanoliter quantities of DNA diagnostic products generated in primer oligo base extension reactions from PCR templates were transferred to chips and analyzed by MALDI-TOF MS, giving accurate genotyping results for single base mutations and short tandem repeat polymorphisms (microsatellites). These procedures provide enabling capabilities for extremely accurate high-throughput DNA diagnostics and sequencing based on mass spectrometry.