A method of matching a precursor ion with one or more related product ions comprising: providing, using a processor, a plurality of input data sets, wherein each of said plurality of input data sets is obtained from a different one of a plurality of injections, each of said plurality of input data sets including a same precursor ion having a first retention time, and one or more product ions having a retention time within a time window of error with respect to said first retention time of said precursor ion; selecting, using a processor, from said plurality of input data sets a first input data set in which an intensity of said precursor ion is a maximum with respect to an intensity of said precursor ion in others of said plurality of input data sets; determining, using a processor, a first set of product ions, wherein each product ion in the first set is in the first input data set selected by said selecting and has a retention time within said predetermined retention time window with respect to said first retention time; and for each product ion in said first set, determining, using a processor, as a first result which of said plurality of input data sets include said each product ion having a retention time that is within said time window of error with respect to said first retention time, and determining an intensity sum for said each product ion by summing intensities of said each product ion in said first result whereby each of said intensities of said each product ion that is summed is an intensity of said each product ion in a different one of the plurality of input data sets included in the first result, wherein said first set of product ions are related to said precursor and each of said product ions in said first set has an intensity sum as determined by said step of determining an intensity sum, and ranking the related product ions by intensity sums and selecting a predetermined number of product ions with the maximum intensity sums. providing, using a processor, a plurality of input data sets, wherein each of said plurality of input data sets is obtained from a different one of a plurality of injections, each of said plurality of input data sets including a same precursor ion having a first retention time, and one or more product ions having a retention time within a time window of error with respect to said first retention time of said precursor ion; selecting, using a processor, from said plurality of input data sets a first input data set in which an intensity of said precursor ion is a maximum with respect to an intensity of said precursor ion in others of said plurality of input data sets; determining, using a processor, a first set of product ions, wherein each product ion in the first set is in the first input data set selected by said selecting and has a retention time within said predetermined retention time window with respect to said first retention time; and for each product ion in said first set, determining, using a processor, as a first result which of said plurality of input data sets include said each product ion having a retention time that is within said time window of error with respect to said first retention time, and determining an intensity sum for said each product ion by summing intensities of said each product ion in said first result whereby each of said intensities of said each product ion that is summed is an intensity of said each product ion in a different one of the plurality of input data sets included in the first result, wherein said first set of product ions are related to said precursor and each of said product ions in said first set has an intensity sum as determined by said step of determining an intensity sum, and ranking the related product ions by intensity sums and selecting a predetermined number of product ions with the maximum intensity sums.