1. A method for determining elemental composition of ions from mass spectral data, comprising the steps of: obtaining at least one accurate mass measurement from mass spectral data obtained by using a mass spectrometer; obtaining a search list of candidate elemental compositions whose exact masses fall within a given mass tolerance range from said accurate mass; reporting a probability measure based on a mass error; calculating, using a computer, an isotope pattern for each candidate elemental composition from said search list; constructing a peak component matrix including at least one of said isotope pattern and mass spectral data; performing a regression against at least one of isotope pattern, mass spectral data, and the peak component matrix; reporting a second probability measure for at least one candidate elemental composition based on said isotope pattern regression; and combining the two said probability measures into an overall probability measure through the use of probability multiplications.