Mass spectra are received over time for a compound of interest. A primary XIC is calculated for a primary product ion of the compound and a secondary XIC is calculated for a secondary product ion from the mass spectra. A primary value is calculated from a combination of intensities of one or more points corresponding to one or more times of a primary peak of the primary XIC and a secondary value is calculated from a combination of intensities of one or more points corresponding to the one or more times of a secondary peak of the secondary XIC. Or, the primary value is calculated as an area of a time window within the primary peak and the secondary value is calculated as an area of the time window within the secondary peak. A ratio is calculated from the primary value and the secondary value.

Disclosed are methods for improving compound detection and characterization. Methods for characterizing a sample are disclosed. The methods can include providing a sample to a liquid chromatography system capable of sample separation to generate sample components; analyzing sample components by multiplexed targeted selected ion monitoring (SIM) to generate an inclusion list; and performing iterative mass spectral data-dependent acquisition (DDA) from the inclusion list, to identify individual sample components thereby characterizing the sample. In one example, multiplexed targeted SIMs and iterative MS2 DDA acquisition is used to increase robust compound identification for cell culture medium analysis.

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 chromatogram analysis tool receives blood test data for a sample and divides the data into regions and determines a best-fit match template for each region. The chromatogram analysis tool determines a best-fit match for each region by comparing the blood test data to a set of templates associated with archetypical shapes of the region. The template with the highest r-squared value for the blood test data is the best-fit template. The chromatogram analysis tool generates a report based on the best-fit match templates for each region, which can indicate medical conditions or recommendations for additional testing.

Analytical methods that can be employed to reliably separate known or suspected allergens in a complex mixture of fragrance ingredients are described.

A method, mass spectrometer and computer readable medium for acquiring mass spectral data in raw profile; detecting presence of compounds and relevant time window; performing multivariate statistical analysis of raw profile data in a time window to determine compounds; obtaining separation time profiles for detected compounds containing respective time locations in a time window; and computing pure mass spectra for compounds based on separation time profiles or time locations. A method, mass spectrometer and computer readable medium for acquiring mass spectral data in raw profile of a known and unknown sample; combining mass spectral scans for a sample into a single mass spectrum across a separation time window; performing multivariate statistical analysis of the acquired mass spectral data and computing a distance measure between the known and unknown sample; and using the distance measure as an indication for an unknown sample belonging to a known sample or sample group.

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.

An analysis system includes a separation system that provides compounds to a sample cell of a spectrometric system. The system analyzes spectral information from the spectrometric system by optimizing retention windows for the compounds and identifies quantities of the compounds by comparing spectral information within and outside the respective retention windows. Information is displayed in windows of a user interface.

An exemplary chromatographic alignment system accesses a target file including data representative of a plurality of chromatographic features detected from a first sample and a reference file including data representative of a plurality of chromatographic features detected from a second sample. The system identifies, based on the target and reference files, a distinct retention time offset value for each chromatographic feature included in a first subset of the plurality of chromatographic features detected from the first sample. The system determines, based on the identified distinct retention time offset values for the chromatographic features included in the first subset and on a machine learning model, a distinct predicted retention time offset value for each chromatographic feature included in a second subset of the plurality of chromatographic features detected from the first sample. The system assigns the distinct predicted retention time offset value for each chromatographic feature included in the second subset.

A method, mass spectrometer and computer readable medium for acquiring mass spectral data; comprising acquiring mass spectral data in a raw profile mode; selecting a relevant time window for presence of compounds of interest; performing multivariate statistical analysis of mass spectral raw profile mode data in a time window to determine the number of compounds present; computing a pure profile mode mass spectra for all compounds of interest corresponding to their respective separation time profiles or time locations; searching a mass spectral library for the identification of the compounds; and adding the correctly identified compounds and corresponding profile mode mass spectra to existing mass spectral library and/or newly created profile mode mass spectral library. Implementation can be on a server located amongst a network, such as the internet, of computers, devices, and MS instruments. Users are exposed to advertising relevant to the compounds analyzed and can obtain subscriptions to library updates.