Automated spectral library retention time correction

A system for automatically calculating a regression function to describe how the theoretical retention times of the theoretical product ions of known compounds are varied by the sample in a tandem mass spectrometry data independent acquisition (DIA) experiment, comprising:

• a separation device that separates a plurality of compounds from a sample over time;
• an ion source that receives the plurality of compounds from the separation device and ionizes the plurality of compounds, producing an ion beam of precursor ions;
• a tandem mass spectrometer that receives the ion beam, divides a mass-to-charge ratio (m/z) range of the ion beam into two or more precursor ion mass selection windows, and selects and fragments the two or more precursor ion mass selection windows during each cycle of a plurality of cycles, producing a plurality of measured product ion spectra;
• and
• a processor in communication with the tandem mass spectrometer that
• (a) receives the plurality of measured product ion spectra from the tandem mass spectrometer,
• (b) retrieves a plurality of known compounds from a database,
• (c) for each known compound of the plurality of known compounds, theoretically fragments the known compound producing one or more theoretical product ions,
• (d) for each product ion of each known compound of the database, calculates an extracted ion chromatogram (XIC) from the plurality of measured product ion spectra,
• (e) groups XIC peaks with an intensity above a predetermined intensity threshold value from the XICs calculated for each known compound of the database by the measured retention time, producing one or more measured XIC peak groups for a subset of known compounds of the database that have measured XIC peaks with an intensity above the predetermined intensity threshold value,
• (f) calculates a theoretical retention time for each known compound of the subset of known compounds, and
• (g) calculates a regression function to describe how the known retention times of the database are varied in the sample using the theoretical retention times of the subset of known compounds as the independent variables and using the measured retention times of the measured XIC peak groups of the subset of known compounds as the dependent variables.

A method for automatically calculating a regression function to describe how the known retention times of a spectral library of known compounds are varied by the sample in a tandem mass spectrometry data independent acquisition (DIA) experiment, comprising:

• (a) receiving a plurality of measured product ion spectra from a tandem mass spectrometer using a processor,
• wherein the plurality of measured product ion spectra are produced by the tandem mass spectrometer by dividing a mass-to-charge ratio (m/z) range of an ion beam into two or more precursor ion mass selection windows and selecting and fragmenting the two or more precursor ion mass selection windows during each cycle of a plurality of cycles,
• wherein the ion beam is produced by an ion source that ionizes a plurality of compounds, producing an ion beam of precursor ions, and
• wherein the plurality of compounds is separated from a sample by a separation device;
• (b) retrieving from a spectral library of known compounds one or more product ions for each known compound using the processor;
• (c) for each product ion of each known compound of the spectral library, calculating an extracted ion chromatogram (XIC) from the plurality of measured product ion spectra using the processor;
• (d) grouping XIC peaks with an intensity above a predetermined intensity threshold value from the XICs calculated for each known compound of the spectral library by the measured retention time using the processor, producing one or more measured XIC peak groups for a subset of known compounds of the spectral library that have measured XIC peaks with an intensity above the predetermined intensity threshold value;
• (e) retrieving from the spectral library a known retention time for each known compound of the subset of known compounds using the processor;
• and
• (f) calculating a regression function to describe how the known retention times of the spectral library are varied in the sample using the known retention times of the subset of known compounds as the independent variables and using the measured retention times of the measured XIC peak groups of the subset of known compounds as the dependent variables using the processor.