Method for enhancing information in dda mass spectrometry

A method for performing a data-dependent acquisition (DDA) mass spectrometry experiment, comprising:

• instructing an ion source device to ionize one or more compounds of a sample using a processor, producing an ion beam;
• instructing a tandem mass spectrometer to transmit a mass range of precursor ions from the ion beam using the processor;
• instructing a mass analyzer of the tandem mass spectrometer to measure a precursor ion mass spectrum for the mass range using the processor,
• selecting one or more peaks of the mass spectrum for a peak list using the processor;
• and for each precursor ion peak of the peak list,
• selecting a peak mass range including the precursor ion peak using the processor,
• instructing a mass filter of the tandem mass spectrometer to scan a precursor ion mass selection window with a width smaller than the peak mass range across the peak mass range in overlapping steps using the processor, producing a series of overlapping precursor ion mass selection windows across the peak mass range,
• instructing the fragmentation device to fragment each overlapping precursor ion mass selection window of the series using the processor, and
• instructing the mass analyzer to mass analyze product ions produced from each overlapping precursor ion mass selection window of the series using the processor, producing a product ion spectrum for each overlapping precursor ion mass selection window of the series and a plurality of product ion spectra for the peak.

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 performing a data-dependent acquisition (DDA) mass spectrometry experiment, 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 an ion source device to ionize one or more compounds of a sample using the control module, producing an ion beam;
• instructing a tandem mass spectrometer to transmit a mass range of precursor ions from the ion beam using the control module;
• instructing a mass analyzer of the tandem mass spectrometer to measure a precursor ion mass spectrum for the mass range using the control module,
• selecting one or more peaks of the mass spectrum for a peak list using the analysis module;
• and
• for each precursor ion peak of the peak list,
• selecting a peak mass range including the precursor ion peak using the analysis module,
• instructing a mass filter of the tandem mass spectrometer to scan a precursor ion mass selection window with a width smaller than the peak mass range across the peak mass range in overlapping steps using the control module, producing a series of overlapping precursor ion mass selection windows across the peak mass range,
• instructing the fragmentation device to fragment each overlapping precursor ion mass selection window of the series using the control module, and
• instructing the mass analyzer to mass analyze product ions produced from each overlapping precursor ion mass selection window of the series using the control module, producing a product ion spectrum for each overlapping precursor ion mass selection window of the series and a plurality of product ion spectra for the peak.