Threshold-based IDA exclusion list

A method for excluding from a peak list in an information dependent acquisition (IDA) mass spectrometry experiment endogenous background ions that have the same mass-to-charge ratio (m/z) as metabolite ions, comprising:

• receiving an ion beam from an ion source device produced by ionizing a control sample that does not include a metabolite compound using a tandem mass spectrometer;
• performing a mass spectrometry (MS) scan of a mass range on the ion beam producing background peak m/z and intensity values for background precursor ions using the tandem mass spectrometer;
• selecting one or more of the background peaks of the background precursor ions for an exclusion list and including in the exclusion list an m/z value and an intensity value for each background peak of the selected one or more background peaks using the tandem mass spectrometer;
• receiving an ion beam from the ion source device produced by ionizing an experimental sample that does include the metabolite compound using the tandem mass spectrometer;
• performing an MS scan of the mass range on the ion beam producing peak m/z and intensity values for precursor ions using the tandem mass spectrometer;
• selecting one or more of the peaks of the precursor ions for a peak list and including in the peak list an m/z value and an intensity value for each peak of the selected one or more peaks using the tandem mass spectrometer;
• scaling the peak list or the exclusion list by:
• selecting one known background peak that is on the peak list and the exclusion list,
• calculating a ratio of the intensity value of the one known background peak on the peak list and the intensity value of the one known background peak on the exclusion list, and
• multiplying each intensity value on the peak list or the exclusion list by the ratio;
• and
• excluding, after scaling the peak list or the exclusion list, from the peak list each peak that has both an m/z value and an intensity value that correspond to an m/z value and an intensity value of a background peak of the exclusion list using the tandem mass spectrometer.

A computer program product, comprising a non-transitory and tangible computer-readable storage medium whose contents include a program with instructions being executed on a processor so as to perform a method for excluding from a peak list in an information dependent acquisition (IDA) mass spectrometry experiment endogenous background ions that have the same mass-to-charge ratio (m/z) as metabolite ions, the method comprising:

• providing a system, wherein the system comprises one or more distinct software modules, and wherein the distinct software modules comprise a control module and an analysis module;
• instructing a tandem mass spectrometer to receive an ion beam from an ion source device produced by ionizing a control sample that does not include a metabolite compound using the control module;
• instructing the tandem mass spectrometer to perform a mass spectrometry (MS) scan of a mass range on the ion beam producing background peak m/z and intensity values for background precursor ions using the control module;
• selecting one or more of the background peaks of the background precursor ions for an exclusion list and including in the exclusion list an m/z value and an intensity value for each background peak of the selected one or more background peaks using the analysis module;
• instructing the tandem mass spectrometer to receive an ion beam from the ion source device produced by ionizing an experimental sample that does include the metabolite compound using the control module;
• instructing the tandem mass spectrometer to perform an MS scan of the mass range on the ion beam producing peak m/z and intensity values for precursor ions using the control module;
• selecting one or more of the peaks of the precursor ions for a peak list and including in the peak list an m/z value and an intensity value for each peak of the selected one or more peaks using the analysis module;
• scaling the peak list or the exclusion list by:
• selecting one known background peak that is on the peak list and the exclusion list,
• calculating a ratio of the intensity value of the one known background peak on the peak list and the intensity value of the one known background peak on the exclusion list, and
• multiplying each intensity value on the peak list or the exclusion list by the ratio;
• and
• excluding, after scaling the peak list or the exclusion list, from the peak list each peak that has both an m/z value and an intensity value that correspond to an m/z value and an intensity value of a background peak of the exclusion list using the analysis module.