A system for sequential windowed acquisition of mass spectrometry data, comprising: a mass spectrometer that includes a linear ion trap, a collision cell and a mass analyzer; and a processor in communication with the mass spectrometer configured to: receive a mass range and a mass window width parameter for a sample, instruct the mass spectrometer to transmit by the linear ion trap a plurality of selected ions from an ion beam from the sample, the selected ions being within the mass range, to thereby fill the collision cell with said selected ions and to allow the selected ions to cool, instruct the mass spectrometer to turn off the ion beam, instruct the mass spectrometer to transfer back the selected ions within the mass range from the collision cell into the linear ion trap, calculate two or more adjacent or overlapping mass windows that span a mass range using the mass window width parameter, instruct the mass spectrometer to apply an RF excitation waveform to the linear ion trap to select ions within each of the two or more adjacent or overlapping mass windows, instruct the mass spectrometer to eject the selected ions within each of the two or more adjacent or overlapping mass windows from the linear ion trap into the collision cell, instruct the mass spectrometer to fragment the selected ions within each of the two or more adjacent or overlapping mass windows in the collision cell, and instruct the mass spectrometer to detect a mass spectrum from the fragment ions of the each mass window with the mass analyzer, producing a collection of mass spectra for the mass range. a mass spectrometer that includes a linear ion trap, a collision cell and a mass analyzer; and a processor in communication with the mass spectrometer configured to: receive a mass range and a mass window width parameter for a sample, instruct the mass spectrometer to transmit by the linear ion trap a plurality of selected ions from an ion beam from the sample, the selected ions being within the mass range, to thereby fill the collision cell with said selected ions and to allow the selected ions to cool, instruct the mass spectrometer to turn off the ion beam, instruct the mass spectrometer to transfer back the selected ions within the mass range from the collision cell into the linear ion trap, calculate two or more adjacent or overlapping mass windows that span a mass range using the mass window width parameter, instruct the mass spectrometer to apply an RF excitation waveform to the linear ion trap to select ions within each of the two or more adjacent or overlapping mass windows, instruct the mass spectrometer to eject the selected ions within each of the two or more adjacent or overlapping mass windows from the linear ion trap into the collision cell, instruct the mass spectrometer to fragment the selected ions within each of the two or more adjacent or overlapping mass windows in the collision cell, and instruct the mass spectrometer to detect a mass spectrum from the fragment ions of the each mass window with the mass analyzer, producing a collection of mass spectra for the mass range. receive a mass range and a mass window width parameter for a sample, instruct the mass spectrometer to transmit by the linear ion trap a plurality of selected ions from an ion beam from the sample, the selected ions being within the mass range, to thereby fill the collision cell with said selected ions and to allow the selected ions to cool, instruct the mass spectrometer to turn off the ion beam, instruct the mass spectrometer to transfer back the selected ions within the mass range from the collision cell into the linear ion trap, calculate two or more adjacent or overlapping mass windows that span a mass range using the mass window width parameter, instruct the mass spectrometer to apply an RF excitation waveform to the linear ion trap to select ions within each of the two or more adjacent or overlapping mass windows, instruct the mass spectrometer to eject the selected ions within each of the two or more adjacent or overlapping mass windows from the linear ion trap into the collision cell, instruct the mass spectrometer to fragment the selected ions within each of the two or more adjacent or overlapping mass windows in the collision cell, and instruct the mass spectrometer to detect a mass spectrum from the fragment ions of the each mass window with the mass analyzer, producing a collection of mass spectra for the mass range.