A method of analyzing a sample containing multiple analytes to determine both the separation time and mass to charge ratio ( m / z) for each analyte comprising the steps of: (a) providing a separation device that separates the individual analytes over a period of time by virtue of some physical and/or chemical characteristic other than the mass to charge ratio, (b) providing a mass spectrometer that determines the mass to charge ratio of individual analytes at a rate that is slower than the temporal width of an analyte packet/band in the separation device, (c) introducing multiple portions of the sample into the separation device at known time intervals following an encoded sequence, (d) separating individual analytes within each portion of the sample in the separation device, thereby producing a flow of the separated analytes out of the separation device, (e) dividing the flow of separated analytes exiting the separation device into a series of temporal windows, each of the temporal windows consisting of the flow of separated analytes exiting the separation device during a period of time shorter than the shortest peak width of the individual analytes, and beginning at a known time interval from the introduction of at least one of the multiple portions of the sample injected into the separation device, (f) introducing analytes from the series of temporal windows into the mass spectrometer, wherein ions outside of said series of temporal windows are not introduced into the mass spectrometer and are instead blocked by an ion gate, (g) acquiring an m / z spectrum of all the analytes which were transmitted through all the temporal windows (h) repeating steps c) to g) at different time intervals from the introduction of at least one of the multiple portions of the sample injected into the separation device (i) determining the encoded separation and m / z spectra of the separated analytes transmitted to the mass spectrometer, (j) decoding the encoded separation and mass spectra using an inverse matrix transform. (a) providing a separation device that separates the individual analytes over a period of time by virtue of some physical and/or chemical characteristic other than the mass to charge ratio, (b) providing a mass spectrometer that determines the mass to charge ratio of individual analytes at a rate that is slower than the temporal width of an analyte packet/band in the separation device, (c) introducing multiple portions of the sample into the separation device at known time intervals following an encoded sequence, (d) separating individual analytes within each portion of the sample in the separation device, thereby producing a flow of the separated analytes out of the separation device, (e) dividing the flow of separated analytes exiting the separation device into a series of temporal windows, each of the temporal windows consisting of the flow of separated analytes exiting the separation device during a period of time shorter than the shortest peak width of the individual analytes, and beginning at a known time interval from the introduction of at least one of the multiple portions of the sample injected into the separation device, (f) introducing analytes from the series of temporal windows into the mass spectrometer, wherein ions outside of said series of temporal windows are not introduced into the mass spectrometer and are instead blocked by an ion gate, (g) acquiring an m / z spectrum of all the analytes which were transmitted through all the temporal windows (h) repeating steps c) to g) at different time intervals from the introduction of at least one of the multiple portions of the sample injected into the separation device (i) determining the encoded separation and m / z spectra of the separated analytes transmitted to the mass spectrometer, (j) decoding the encoded separation and mass spectra using an inverse matrix transform.