A system for automatically triggering a dependent mass spectrometry scan for a background signal during data acquisition, comprising: a separation device that is configured to separate one or more compounds from a sample mixture; a mass spectrometer that is configured to perform a mass spectrometry scan on the separating sample mixture at a plurality of intervals; and a processor that is configured to: receive from the mass spectrometer each mass spectrometry scan at each interval of the plurality of intervals, determine at a first interval of the plurality of intervals that a received mass spectrometry scan at the first interval and one or more preceding received mass spectrometry scans include a varying ion signal that represents an ion of a compound of interest and that has an intensity above a threshold level, instruct the mass spectrometer to perform a dependent mass spectrometry scan of said ion of the compound of interest at the first interval producing a spectrum for the compound of interest, select a second interval of the plurality of intervals that is after the first interval and that is after the varying ion signal has an intensity that has decreased to a value below the threshold level, instruct the mass spectrometer to perform a dependent mass spectrometry scan of said ion of the compound of interest at the second interval producing a spectrum for the background, wherein the dependent mass spectrometry scans are of the same type; and calculate a corrected spectrum for the compound of interest by subtracting the spectrum for the background from the spectrum for the compound of interest. a separation device that is configured to separate one or more compounds from a sample mixture; a mass spectrometer that is configured to perform a mass spectrometry scan on the separating sample mixture at a plurality of intervals; and a processor that is configured to: receive from the mass spectrometer each mass spectrometry scan at each interval of the plurality of intervals, determine at a first interval of the plurality of intervals that a received mass spectrometry scan at the first interval and one or more preceding received mass spectrometry scans include a varying ion signal that represents an ion of a compound of interest and that has an intensity above a threshold level, instruct the mass spectrometer to perform a dependent mass spectrometry scan of said ion of the compound of interest at the first interval producing a spectrum for the compound of interest, select a second interval of the plurality of intervals that is after the first interval and that is after the varying ion signal has an intensity that has decreased to a value below the threshold level, instruct the mass spectrometer to perform a dependent mass spectrometry scan of said ion of the compound of interest at the second interval producing a spectrum for the background, wherein the dependent mass spectrometry scans are of the same type; and calculate a corrected spectrum for the compound of interest by subtracting the spectrum for the background from the spectrum for the compound of interest. receive from the mass spectrometer each mass spectrometry scan at each interval of the plurality of intervals, determine at a first interval of the plurality of intervals that a received mass spectrometry scan at the first interval and one or more preceding received mass spectrometry scans include a varying ion signal that represents an ion of a compound of interest and that has an intensity above a threshold level, instruct the mass spectrometer to perform a dependent mass spectrometry scan of said ion of the compound of interest at the first interval producing a spectrum for the compound of interest, select a second interval of the plurality of intervals that is after the first interval and that is after the varying ion signal has an intensity that has decreased to a value below the threshold level, instruct the mass spectrometer to perform a dependent mass spectrometry scan of said ion of the compound of interest at the second interval producing a spectrum for the background, wherein the dependent mass spectrometry scans are of the same type; and calculate a corrected spectrum for the compound of interest by subtracting the spectrum for the background from the spectrum for the compound of interest.