A method of acquiring and analyzing mass spectra of a sample comprising: delivering the sample into an ion source of a mass spectrometer (103, 203) and generating first-generation ions from the sample using the ion source; repeatedly performing a cycle comprising: acquiring a series of survey mass spectra of the first-generation ions using a mass analyzer of the mass spectrometer (104, 204); acquiring a series of fragment-ion mass spectra using the mass spectrometer (108, 208), wherein each of the survey mass spectra acquired during an individual cycle comprises a respective sub-range of m/z values (42a-d 46a-d, 52a-e) of the range of interest of m/z values and wherein at least one gap exists in the mass spectra coverage of the first-generation ions, each fragment-ion spectrum comprising a record of a respective set of fragment-ion species generated by fragmentation of a respective subset of the first-generation ions (44, 54), said respective subset of the first-generation ions comprising a respective isolated range of mass-to-charge ratio ( m / z) values, the series of isolated ranges, taken together, including all m / z values within a range of interest of m / z values; dividing the acquired series of fragment-ion mass spectra into a first group and a second group (116, 216), wherein an appearance of a fragment-ion species signature observed in each fragment-ion mass spectrum of the first group correlates with the appearance of a first-generation ion species signature observed in a survey mass spectrum and wherein, in the second group, no correlation is observed between signatures of fragment-ion species and signatures of first-generation ion species; and mathematically processing the fragment-ion spectra of the first and second groups by different mathematical processing procedures (118, 218), wherein at least one mass spectrometer operational parameter used to acquire at least one of the survey mass spectra is adjusted based on results of an earlier-acquired one of the survey mass spectra (120, 220), wherein the fragment-ion spectra of the first group are mathematically processed by reference to at least one database comprising lists of fragment-ion species m / z values that generated by fragmentation of precursor-ion species of known fragment-ion species m / z values and wherein the fragment-ion spectra of the second group are mathematically processed without reference to any precursor-ion species. delivering the sample into an ion source of a mass spectrometer (103, 203) and generating first-generation ions from the sample using the ion source; repeatedly performing a cycle comprising: acquiring a series of survey mass spectra of the first-generation ions using a mass analyzer of the mass spectrometer (104, 204); acquiring a series of fragment-ion mass spectra using the mass spectrometer (108, 208), acquiring a series of survey mass spectra of the first-generation ions using a mass analyzer of the mass spectrometer (104, 204); acquiring a series of fragment-ion mass spectra using the mass spectrometer (108, 208), wherein each of the survey mass spectra acquired during an individual cycle comprises a respective sub-range of m/z values (42a-d 46a-d, 52a-e) of the range of interest of m/z values and wherein at least one gap exists in the mass spectra coverage of the first-generation ions, each fragment-ion spectrum comprising a record of a respective set of fragment-ion species generated by fragmentation of a respective subset of the first-generation ions (44, 54), said respective subset of the first-generation ions comprising a respective isolated range of mass-to-charge ratio ( m / z) values, the series of isolated ranges, taken together, including all m / z values within a range of interest of m / z values; acquired during an individual cycle comprises a respective sub-range of m/z values (42a-d 46a-d, 52a-e) of the range of interest of m/z values and wherein at least one gap exists in the mass spectra coverage of the first-generation ions, each fragment-ion spectrum comprising a record of a respective set of fragment-ion species generated by fragmentation of a respective subset of the first-generation ions (44, 54), said respective subset of the first-generation ions comprising a respective isolated range of mass-to-charge ratio ( m / z) values, the series of isolated ranges, taken together, including all m / z values within a range of interest of m / z values; dividing the acquired series of fragment-ion mass spectra into a first group and a second group (116, 216), wherein an appearance of a fragment-ion species signature observed in each fragment-ion mass spectrum of the first group correlates with the appearance of a first-generation ion species signature observed in a survey mass spectrum and wherein, in the second group, no correlation is observed between signatures of fragment-ion species and signatures of first-generation ion species; and mathematically processing the fragment-ion spectra of the first and second groups by different mathematical processing procedures (118, 218), wherein at least one mass spectrometer operational parameter used to acquire at least one of the survey mass spectra is adjusted based on results of an earlier-acquired one of the survey mass spectra (120, 220), wherein the fragment-ion spectra of the first group are mathematically processed by reference to at least one database comprising lists of fragment-ion species m / z values that generated by fragmentation of precursor-ion species of known fragment-ion species m / z values and wherein the fragment-ion spectra of the second group are mathematically processed without reference to any precursor-ion species.