A system for identifying missing product ions after demultiplexing product ion spectra produced by overlapping precursor ion transmission windows in sequential windowed acquisition tandem mass spectrometry, comprising: a tandem mass spectrometer that performs overlapping sequential windowed acquisition on a sample by on each cycle, stepping a precursor mass window across a mass range, fragmenting transmitted precursor ions of each stepped precursor mass window, and analyzing product ions produced from the fragmented transmitted precursor ions, and between at least two cycles, shifting the stepped precursor mass window to produce overlapping mass windows between the at least two cycles, wherein the overlapping sequential windowed acquisition produces a product ion spectrum for each stepped precursor mass window for each cycle of the at least two cycles; and a processor in communication with the tandem mass spectrometer that receives a plurality of overlapping stepped precursor mass windows and their corresponding product ion spectra for the at least two cycles from the tandem mass spectrometer, selects a first precursor mass window and the corresponding first product ion spectrum from the plurality of overlapping stepped precursor mass windows and their corresponding product ion spectra, and demultiplexes a product ion spectrum for each overlapped portion of the first precursor mass window producing two or more demultiplexed first product ion spectra for the first precursor mass window by for each overlapped portion of the first precursor mass window, (a) adding the first product ion spectrum and a product ion spectrum of an overlapping precursor mass window producing a summed product ion spectrum and (b) subtracting product ion spectra of two or more precursor mass windows adjacent to the first precursor mass window and the overlapping precursor mass window that overlap with non-overlapping portions of the first precursor mass window and the overlapping precursor mass window from the summed product ion spectrum one or more times, adds the two or more demultiplexed first product ion spectra together producing a reconstructed summed demultiplexed first product ion spectrum, and identifies missing product ions in the summed demultiplexed first product ion spectrum by comparing the summed demultiplexed first product ion spectrum and the first product ion spectrum. a tandem mass spectrometer that performs overlapping sequential windowed acquisition on a sample by on each cycle, stepping a precursor mass window across a mass range, fragmenting transmitted precursor ions of each stepped precursor mass window, and analyzing product ions produced from the fragmented transmitted precursor ions, and between at least two cycles, shifting the stepped precursor mass window to produce overlapping mass windows between the at least two cycles, wherein the overlapping sequential windowed acquisition produces a product ion spectrum for each stepped precursor mass window for each cycle of the at least two cycles; and a processor in communication with the tandem mass spectrometer that receives a plurality of overlapping stepped precursor mass windows and their corresponding product ion spectra for the at least two cycles from the tandem mass spectrometer, selects a first precursor mass window and the corresponding first product ion spectrum from the plurality of overlapping stepped precursor mass windows and their corresponding product ion spectra, and demultiplexes a product ion spectrum for each overlapped portion of the first precursor mass window producing two or more demultiplexed first product ion spectra for the first precursor mass window by for each overlapped portion of the first precursor mass window, (a) adding the first product ion spectrum and a product ion spectrum of an overlapping precursor mass window producing a summed product ion spectrum and (b) subtracting product ion spectra of two or more precursor mass windows adjacent to the first precursor mass window and the overlapping precursor mass window that overlap with non-overlapping portions of the first precursor mass window and the overlapping precursor mass window from the summed product ion spectrum one or more times, (a) adding the first product ion spectrum and a product ion spectrum of an overlapping precursor mass window producing a summed product ion spectrum and (b) subtracting product ion spectra of two or more precursor mass windows adjacent to the first precursor mass window and the overlapping precursor mass window that overlap with non-overlapping portions of the first precursor mass window and the overlapping precursor mass window from the summed product ion spectrum one or more times, adds the two or more demultiplexed first product ion spectra together producing a reconstructed summed demultiplexed first product ion spectrum, and identifies missing product ions in the summed demultiplexed first product ion spectrum by comparing the summed demultiplexed first product ion spectrum and the first product ion spectrum.