The recent proliferation of electrospray as an ionization method has greatly increased the ability to perform analyses of large biomolecules by using mass spectrometry. The major advantage of electrospray is the ability to produce multiply charged ions, which brings large molecules down to a mass-to-charge ratio range amenable to most instruments. Multiple charging is also a disadvantage because mass (m) becomes ambiguous unless charge (z) can be assigned. This is typically performed with simple algorithms that use multiple peaks of the same m and different z, but these methods are difficult to apply to complex mixtures and not applicable when only one z appears for each m. The use of mass analyzers with higher resolving powers, like the Fourier transform mass spectrometer, allows resolution of isotopic peaks, providing an internal 1-Da mass scale that can be used for unambiguous charge assignment. Manual assignment of charge state from the isotopic peaks is time consuming and becomes inaccurate when either the signal level or resolving power are low. For these cases, computer algorithms based on pattern recognition techniques have been developed to assist in assignment of charge states to isotopic clusters. These routines provide for more rapid analysis with higher accuracy than available manually.