Advances in nucleic acid sample preparation for electrospray ionization and matrix-assisted laser desorption ionization mass spectrometry

Electrospray ionization (ESI) and matrix-assisted laser desorption ionization (MALDI) have revolutionized the field of nucleic acid analysis. These soft ionization techniques facilitate characterization of DNA and RNA biopolymers by mass spectrometry (MS), providing orthogonal and complementary approaches to conventional biochemical methods of nucleic acid analysis. ESI-MS and MALDI-MS are capable of sequencing nucleic acids with single-nucleotide resolution, detecting many chemical modifications, and quantitatively measuring nucleic acid abundance. However, complex biological samples pose challenges for ESI and MALDI due to interfering compounds and untargeted nucleic acids. Large nucleic acids are especially challenging to analyze by ESI and MALDI due to their propensity to form metal adducts and isotopic distributions that convolute and diminish analytical signals. The past two decades have seen sharp increases in the demand for characterizing natural and synthetic nucleic acids beyond the capabilities of conventional sequencing approaches, reinforcing the importance of developing high-throughput, sensitive, and broadly applicable MS methods for DNA and RNA analysis. Innovations in nucleic acid sample preparation for ESI and MALDI including chemical derivatization, nuclease treatment, and stable isotope labeling strategies have been vital to this effort and have delivered timely answers to the most pressing questions in nucleic acid biology. To celebrate the 20th anniversary of the Nobel Prize in Chemistry awarded to soft ionization techniques in 2002, this review summarizes the past two decades of advances in sample preparation methods for nucleic acid analysis by ESI-MS and MALDI-MS.