Mass spectrometry (MS) is becoming the method of choice for quality control (QC) of oligonucleotides. Of the various configurations of mass spectrometry available, Matrix-Assisted Laser Desorption/Ionization-Time Of Flight (MALDI-TOF) is most commonly employed when examining oligos. MALDI-TOF instrumentation is suitable for use in a high-throughput industrial QC setting and can resolve molecules in the size range of oligonucleotides. While small compared to nucleic acids from biologic sources, oligonucleotides are nevertheless relatively large molecules, ranging in size from about 6000 daltons for a 20-mer to 30,000 daltons for a 100-mer. MALDI-TOF is useful for compounds up to ~15,000 daltons, or about a 50-mer oligonucleotide. Samples >15,000 daltons do not ionize/fly effectively and, additionally, are outside the optimal resolution range of these instruments. Electrospray Ionization - Time of Flight (ESI-TOF) MS can resolve longer oligonucleotides (up to ~80 bases in length).
The Underlying Technology
The oligonucleotide test sample is mixed with a carrier or matrix (picolinic acid) and is deposited on a grid. The MALDI-TOF instrument uses pulses of laser light to vaporize the oligo/matrix in a process known as "desorption". During this process, some molecules become ionized through protonation (i.e., the oligo gains a proton and becomes 1+ charge). The laser pulse can also fragment the molecule into a variety of charged and neutral particles (which can lead to spurious bands or artifacts in the resulting spectrum).
In time of flight (TOF) mass spectrometry, ionized oligo molecules are accelerated by an electrostatic field in the mass analyzer to a common kinetic energy. With the same kinetic energy, lighter ions travel faster and heavier ions travel more slowly. The ionized particles enter at one end of the TOF tube, and the number of ions reaching a detector at the other end is recorded in a time-dependent manner. The lightest ions reach the detector first and the heaviest arrive last. The entire mass spectrum is recorded in a fraction of a second as ion flux versus time.