A system for reconstructing a separation profile of a precursor ion in a tandem mass spectrometry experiment from multiple scans across a mass range, the system comprising: a separation device that is configured to separate ions from a sample; a mass filter that is configured to receive the ions from the separation device and filter the ions by, in each of two or more scans across a mass range, moving a transmission window that has a constant rate of precursor ion transmission for each precursor ion in small steps across the mass range so that there is a large overlap between successive transmission windows, to produce a series of overlapping transmission windows across the mass range for each scan of the two or more scans, and wherein when intensities of product ions produced from precursor ions filtered by the overlapping transmission windows are plotted as a function of the transmission window moving across the mass range, each product ion has an intensity for the same mass range in which its precursor ion has been transmitted; a fragmentation device that is configured to fragment the precursor ions produced at each step; a mass analyzer that is configured to analyze resulting product ions, to produce a product ion spectrum for each step of the transmission window and a plurality of product ion spectra for the mass range for the each scan; and a processor in communication with the mass filter and the mass analyzer that is configured to: receive the plurality of product ion spectra produced by the series of overlapping transmission windows for the each scan, producing a plurality of multi-scan product ion spectra, select at least one product ion from the plurality of multi-scan product ion spectra that is present at least two or more times in product ion spectra from each of two or more scans, and fit a known separation profile of a precursor ion to intensities from the at least one product ion in the plurality of multi-scan product ion spectra to reconstruct a separation profile of a precursor ion of the at least one product ion. a separation device that is configured to separate ions from a sample; a mass filter that is configured to receive the ions from the separation device and filter the ions by, in each of two or more scans across a mass range, moving a transmission window that has a constant rate of precursor ion transmission for each precursor ion in small steps across the mass range so that there is a large overlap between successive transmission windows, to produce a series of overlapping transmission windows across the mass range for each scan of the two or more scans, and wherein when intensities of product ions produced from precursor ions filtered by the overlapping transmission windows are plotted as a function of the transmission window moving across the mass range, each product ion has an intensity for the same mass range in which its precursor ion has been transmitted; a fragmentation device that is configured to fragment the precursor ions produced at each step; a mass analyzer that is configured to analyze resulting product ions, to produce a product ion spectrum for each step of the transmission window and a plurality of product ion spectra for the mass range for the each scan; and a processor in communication with the mass filter and the mass analyzer that is configured to: receive the plurality of product ion spectra produced by the series of overlapping transmission windows for the each scan, producing a plurality of multi-scan product ion spectra, select at least one product ion from the plurality of multi-scan product ion spectra that is present at least two or more times in product ion spectra from each of two or more scans, and fit a known separation profile of a precursor ion to intensities from the at least one product ion in the plurality of multi-scan product ion spectra to reconstruct a separation profile of a precursor ion of the at least one product ion. receive the plurality of product ion spectra produced by the series of overlapping transmission windows for the each scan, producing a plurality of multi-scan product ion spectra, select at least one product ion from the plurality of multi-scan product ion spectra that is present at least two or more times in product ion spectra from each of two or more scans, and fit a known separation profile of a precursor ion to intensities from the at least one product ion in the plurality of multi-scan product ion spectra to reconstruct a separation profile of a precursor ion of the at least one product ion.