For small singly charged ions, Fourier transform mass spectrometry (FTMS) has demonstrated the ability to perform multistage mass spectral experiments (MS”) with high resolu-tion and high mass accuracy using collisionally activated dissociation (CAD). The combination of electrospray ionization (ESI) with the FTMS provides the potential to extend these capabilities for structural characterization of large biomolecules. The standard FTMS-CAD method is problem-atic in that it is inefficient and produces ions well away from the center of the cell. More efficient collisional methods have been demonstrated for small molecules (sustained off-resonance irradiation (SORI) CAD, very low energy (VLE) CAD, multiple excitation collisional activation (MECA)) that provide the additional benefit of producing product ions closer tothe center of the trapped ion cell. The efficiency (> 92%) for producing sequence-informative peaks from large multiply charged ions is far better than standard CAD. Disadvantages, such as blind spots where no product ions are observed, and isotopic distortions which can cause an incorrect mass assignment, must be considered when methods designed for small singly charged ions are applied to large multiply charged ions. SORI provided the highest efficiency, selectivity, and resolving power (9 X 10s) for product ion spectra and is recommended for most applications because of its ease of implementation.

New techniquessuch as electrospray ionization (ESI) 1· 1 2 and matrix-assisted laser desorption/ionization (MALDI) 3 have made possible accurate molecular weight determinations for large biological molecules. ESI has the particular benefit that multiple charging shifts the signal of molecules as large as 200 kDa down to the m/z range accessible with most mass analyzers. 4 Tandem mass spectrometry (MS/MS) dissocia-