High-fidelity genotyping and therapeutic oligonucleotides analysis by liquid-phase ion trap coupled with mass spectrometry.

Rapid and accurate nucleic acid analysis is essential for disease diagnostics and drug development, yet persistent metal cation interference severely limits mass spectrometry's effectiveness. We developed a liquid-phase ion trap (LPIT) system that utilizes strong electric fields to simultaneously dissociate metal contaminants and enrich purified nucleic acid ions directly in solution. This dual-action mechanism simplifies complex mass spectra, achieving up to a 48-fold improvement in mass accuracy and a 100-fold enhancement in signal intensity for intact DNA molecules. The platform's versatility was demonstrated through high-resolution genetic variation analysis, rapid influenza virus subtyping from raw PCR products, and precise impurity detection in therapeutic drugs. By eliminating laborious pretreatment, the LPIT-ESI-MS system establishes a robust platform for high-fidelity genotyping and the rigorous analysis of therapeutic oligonucleotides, accelerating both clinical diagnostics and biopharmaceutical quality control.