Rapid Extraction and Structural Characterization of Biomolecules in Agarose Gels by Laser Desorption Fourier Transform Mass Spectrometry

A method originally developed for the extraction of biomolecules from agarose gel slices has been utilized as a rapid means of isolating biological compounds from gels for subsequent structural characterization by matrix-assisted laser desorption-ionization Fourier transform mass spectrometry (MALDI/FTMS). This “freeze-squeeze” extraction method involves pressure extrusion of fluid from frozen gel slices and provides near 50% recovery of analyte in less than 5 min. Experiments were directed at examining the recovery efficiency of the extraction method using ¹⁴Clabeled adenosine monophosphate and investigating the effect of high buffer concentrations on the laser desorption mass spectra. When coupled with this extraction technique, MALDI/FTMS can be used to detect and identify biomolecules at the low picomole level in agarose gel slices. The accurate mass measurements and MS/MS capabilities of the FTMS were exploited to provide detailed structural information at the isomeric level for oligonucleotides electrophoresed into agarose gels.