Acquisition Strategy for Top-Down Analysis with Reduced Background and Peak Overlapping

A method for separating ions measured by a mass analyzer into two or more mass spectra based on charge state using a single electron multiplier analog-to-digital conversion (ADC) detector, comprising:

• instructing a mass analyzer of a mass spectrometer to detect a pulse for each ion impacting an electron multiplier ADC detector of the mass analyzer using a processor, wherein each ion impacting the ADC detector is from a plurality of ions that are transmitted to the mass analyzer by the mass spectrometer and wherein the ADC detector produces detection pulses for detected ions with intensities that are proportional to ion charge state;
• calculating a peak for each pulse detected using peak finding using the processor;
• calculating an intensity for each peak using the processor;
• comparing the intensity of each peak to two or more different predetermined intensity ranges corresponding to two or more different charge state ranges and storing each peak in one of two or more data sets corresponding to the two or more predetermined intensity ranges based on the comparison using the processor;
• and
• creating a mass spectrum for each of the two or more data sets by combining peaks in each data set using the processor, producing two or more mass spectra for ions detected by the mass analyzer based on charge state.

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 separating ions measured by a mass analyzer into two or more mass spectra based on charge state using a single electron multiplier analog-to-digital conversion (ADC) detector, 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 mass analyzer of a mass spectrometer to detect a pulse for each ion impacting an electron multiplier ADC detector of the mass analyzer using the control module, wherein each ion impacting the ADC detector is from a plurality of ions that are transmitted to the mass analyzer by the mass spectrometer and wherein the ADC detector produces detection pulses for detected ions with intensities that are proportional to ion charge state;
• calculating a peak for each pulse detected using peak finding using the analysis module;
• calculating an intensity for each peak using the analysis module;
• comparing the intensity of each peak to two or more different predetermined intensity ranges corresponding to two or more different charge state ranges and storing each peak in one of two or more data sets corresponding to the two or more predetermined intensity ranges based on the comparison using the analysis module;
• and
• creating a mass spectrum for each of the two or more data sets by combining peaks in each data set using the analysis module, producing two or more mass spectra for ions detected by the mass analyzer based on charge state.