Chromatograms and
mass spectra produced by an LC / MS
system are analyzed by creating a two-dimensional
data matrix of the spectral and chromatographic data. The two-dimensional matrix can be created by placing the spectra generated by the
mass spectrometer portion of the LC / MS
system in successive columns of the
data matrix. In this way, the rows of the
data matrix correspond to chromatographic data and the columns of the data matrix correspond to the spectra. A two-dimensional filter is specified and applied to the data matrix to enhance the ability of the
system to detect peaks associated with ions. The two-dimensional filter is specified according to desired criteria. Rank-1 and rank-2 filters can be specified to improve computational efficiency. One method of applying the two-dimensional filter is through
convolution of the data matrix with the two-dimensional filter to produce an output data matrix. Peaks corresponding to detected ions are identified in the output data matrix. Parameters of the peaks are determined and stored for later
processing including quantitation, or simplification of chromatograms or spectra by, for example, identifying peaks associating with ions having retention times falling within a specified
retention time window or having
mass-to charge ratios falling within a specified mass-to-charge ratio window.