AbstractBecause of the high molecular weights and thermal lability of biomolecules such as nucleic acids and protein, they can be difficult to analyze by mass spectrometry. Such analyses require a “soft” ionization method that is capable of generating intact molecular ions. In addition, most mass analyzers have a limited upper mass range that is not sufficient for studying these large molecules. ESI‐MS can be used to analyze molecules with a molecular weight that is larger than the mass‐to‐charge ratio limit of the analyzer. This unit describes how ESI allows for analysis of high‐molecular‐weight compounds through the generation of multiply charged ions in the gas phase. It discusses analyzer configurations, solvent selection, and gives protocols for sample preparation. For applications of ESI‐MS, the unit discusses molecular weight determination and gives protocols for sequencing and for analyzing oligonucleotide modifications.