Systems and methods for identifying precursor and product ion pairs in scanning SWATH data

A system for identifying a precursor ion of a product ion in a scanning data-independent acquisition (DIA) tandem mass spectrometry experiment, comprising:

• a. an ion source device that transforms a sample into an ion beam;
• b. a mass filter that receives the ion beam and filters the ion beam by scanning a precursor ion mass selection window across a precursor ion mass range of interest, producing a series of overlapping precursor ion mass selection windows across the precursor ion mass range;
• c. a fragmentation device that receives the precursor ions of each overlapping precursor ion mass selection window and fragments the precursor ions of each overlapping precursor ion mass selection window;
• d. a mass analyzer that receives the product ions from each fragmentation of each overlapping precursor ion mass selection window and analyzes the resulting product ions, producing a product ion spectrum for each overlapping precursor ion mass selection window and a plurality of product ion spectra for the precursor ion mass range;
• and
• e. a processor in communication with the mass filter and the mass analyzer that
• receives the plurality of product ion spectra produced by the series of overlapping precursor ion mass selection windows,
• selects at least one product ion from the plurality of product ion spectra that has an intensity above a predetermined threshold,
• for the selected product ion, retrieves the intensities of the selected product ion from the plurality of product ion spectra for at least one scan of the precursor ion mass selection window across the precursor ion mass range, producing a trace that describes how the intensity of the selected product ion varies with precursor ion mass-to-charge ratio (m/z) as the precursor ion mass selection window is scanned across the precursor ion mass range,
• creates a matrix multiplication equation that describes how one or more precursor ions corresponds to the trace for the selected product ion, wherein the matrix multiplication equation includes a known n×m mass filter matrix multiplied by an unknown precursor ion column matrix of length m that equates to a selected ion trace column matrix of length n, and
• solves the matrix multiplication equation for the unknown precursor ion column matrix using a numerical method, producing intensities for one or more precursor ion m/z values corresponding to the selected product ion.