A method for identifying an intact protein within a sample containing a plurality of intact proteins using a mass spectrometer, the method comprising: (a) introducing the sample to an ionization source of the mass spectrometer; (b) using the ionization source, generating a plurality of ion species from the plurality of intact proteins, whereby each protein gives rise to a respective subset of the plurality of ion species, wherein each ion species of each subset is a multi-protonated ion species generated from a respective one of the intact proteins; (c) performing a mass analysis of the plurality of ion species using a mass analyzer of the mass spectrometer; (d) automatically recognizing each subset of the plurality of ion species and assigning a charge state, z , to each recognized ion species and a molecular weight, MW, to each intact protein by mathematical analysis of data generated by the mass analysis; (e) selecting a one of the ion species; (f) automatically calculating a collision energy, CE, to be employed for fragmentation of the selected ion species, using the relationship CE D p = c + 1 / k ln 1 / D p − 1 , where D p is a portion of the selected ion species that is desired to remain unfragmented after the fragmentation and c and k are functions only the charge state, z , of the selected ion species and the molecular weight, MW, of the intact protein from which the selected ion species was generated and where c and k are obtained by fitting D p versus collision energy to measurements obtained from known proteins and subsequently fitting c and k to products of powers of MW and z across the data; (g) isolating the selected ion species and fragmenting said species so as to form fragment ion species therefrom using the automatically calculated collision energy; and (h) mass analyzing the fragment ion species. (a) introducing the sample to an ionization source of the mass spectrometer; (b) using the ionization source, generating a plurality of ion species from the plurality of intact proteins, whereby each protein gives rise to a respective subset of the plurality of ion species, wherein each ion species of each subset is a multi-protonated ion species generated from a respective one of the intact proteins; (c) performing a mass analysis of the plurality of ion species using a mass analyzer of the mass spectrometer; (d) automatically recognizing each subset of the plurality of ion species and assigning a charge state, z , to each recognized ion species and a molecular weight, MW, to each intact protein by mathematical analysis of data generated by the mass analysis; (e) selecting a one of the ion species; (f) automatically calculating a collision energy, CE, to be employed for fragmentation of the selected ion species, using the relationship CE D p = c + 1 / k ln 1 / D p − 1 , where D p is a portion of the selected ion species that is desired to remain unfragmented after the fragmentation and c and k are functions only the charge state, z , of the selected ion species and the molecular weight, MW, of the intact protein from which the selected ion species was generated and where c and k are obtained by fitting D p versus collision energy to measurements obtained from known proteins and subsequently fitting c and k to products of powers of MW and z across the data; (g) isolating the selected ion species and fragmenting said species so as to form fragment ion species therefrom using the automatically calculated collision energy; and (h) mass analyzing the fragment ion species. <EOS>