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.