A method, spectral detection system and computer readable medium for acquiring spectral data for a sample containing at least two standard compounds of known retention indices; using the spectral data to select relevant retention time windows corresponding to the at least two standard compounds of known retention indices; building an initial retention index calibration model using the at least two standard compounds of known retention indices; and refining the initial retention index calibration model by one of adding additional or removing existing standard compounds of known retention indices from the calibration model. The calibration model is then used to predict the retention index of an unknown compound from its measured retention time. Both the predicted retention index and the spectral library search are utilized together to indicate the likelihood of a positive compound identification with higher confidence.

Methods are described for the automatic determination and correction of retention time shift of a MS data set relative to a control data set, to correct for retention time drifts endemic to targeted LCMS analyses. In an embodiment, a 2D grid of periodic MS spectra versus time is collected for a control experiment, and RT windows are determined with an additional set of unscheduled mass spectral analyses. During successive experiments, spectra from periodic MS scans are used to determine the correspondence between the current time and the time in the control experiment. The active set of MSn scans to be acquired by the instrument is then determined as the scans with adjusted retention time windows that bracket the corrected retention time.

A gas chromatograph for analyzing content of a gas sample includes a sample gas inlet receiving the sample gas and a carrier gas source providing a carrier gas. A separation column having an inlet and an outlet. A sample valve injects the sample gas and the carrier gas into the separation column inlet at a pressure. Individual component gases in the sample gas separate as they move through the column, and each individual component gas exits the outlet at a component gas retention time which is a function of the individual component gas and the pressure. A detector detects individual component gases as they exit the separation column outlet. A controller coupled to the detector identifies the individual component gases based upon the component gas retention time. The controller calibrates the pressure based upon a component gas retention time.

First data includes chromatogram data consisting of the retention time and the signal intensity of transmitted/absorbed light acquired. Second data is three-dimensional data consisting of the retention time, mass-to-charge ratio and signal intensity. A first retention-time range where a target peak is present and the waveform of the target peak are determined in a chromatogram created from the first data. The number of component peaks within a second retention-time range which corresponds to the first retention-time range in a three-dimensional graph created from the second data is acquired as a measured component-peak number. Model functions whose number equals the measured component-peak number are created, each function involving a peak-width variable representing the width of a component peak. The model functions are gradually modified by adjusting their peak-width variables until the degree of similarity in waveform between the target peak and a model peak expressed by those functions exceeds a threshold.