A method of matching a precursor ion with one or more related product ions comprising: providing a plurality of input data sets obtained from a plurality of injections of an LC/MS analysis, each of said plurality of data sets including a plurality of precursor ions and one or more product ions, the plurality of input data sets based on at least one spectrum obtained from the LC/MS analysis of the plurality of injections; selecting a first data set from among the plurality of input data sets as a reference data set; determining a precursor ion of the plurality of precursor ions in the reference data set at a single retention time, the precursor ion having a precursor ion mass; determining one or more candidate product ions for the precursor ion; for the remaining data sets, determining a corresponding precursor ion and corresponding candidate product ions based on respective retention times and precursor ion masses; aligning said plurality of input data sets in accordance with the single retention time for said precursor ion in a first injection, wherein each precursor ion in each of said plurality of input data sets is aligned at said single retention time and the product ions in said each of said plurality of input data sets are shifted in time in accordance with an amount by which said each precursor ion is shifted by said aligning; for each of said plurality of input data sets, determining which product ions are within a predetermined retention time window with respect to said single retention time for said precursor ion; and if a product ion is within the predetermined retention time window for a specified number of said plurality of input data sets, determining that said product ion is related to said precursor ion having said single retention time; and wherein determining the precursor and product ions in the plurality of input data sets comprises finding sets of masses having a same mass value for said plurality of injections, and a same retention time within said predetermined retention time window within each injection. providing a plurality of input data sets obtained from a plurality of injections of an LC/MS analysis, each of said plurality of data sets including a plurality of precursor ions and one or more product ions, the plurality of input data sets based on at least one spectrum obtained from the LC/MS analysis of the plurality of injections; selecting a first data set from among the plurality of input data sets as a reference data set; determining a precursor ion of the plurality of precursor ions in the reference data set at a single retention time, the precursor ion having a precursor ion mass; determining one or more candidate product ions for the precursor ion; for the remaining data sets, determining a corresponding precursor ion and corresponding candidate product ions based on respective retention times and precursor ion masses; aligning said plurality of input data sets in accordance with the single retention time for said precursor ion in a first injection, wherein each precursor ion in each of said plurality of input data sets is aligned at said single retention time and the product ions in said each of said plurality of input data sets are shifted in time in accordance with an amount by which said each precursor ion is shifted by said aligning; for each of said plurality of input data sets, determining which product ions are within a predetermined retention time window with respect to said single retention time for said precursor ion; and if a product ion is within the predetermined retention time window for a specified number of said plurality of input data sets, determining that said product ion is related to said precursor ion having said single retention time; and wherein determining the precursor and product ions in the plurality of input data sets comprises finding sets of masses having a same mass value for said plurality of injections, and a same retention time within said predetermined retention time window within each injection.