Two-dimensional fourier transform mass analysis in an electrostatic linear ion trap

A method for controlling a mass spectrometer to simultaneously measure precursor and product ion data, comprising:

• controlling ion transfer optics and an ELIT to perform a total number of acquisitions, N, using a processor and, for each acquisition, n, of the N acquisitions,
• controlling the ion transfer optics to inject ions from the ion beam into the ELIT causing the ions to oscillate axially between two electric fields produced by two the sets of reflectrons using the processor, wherein the ion beam is produced by an ion source configured to ionize a sample and wherein the ELIT includes the two sets of reflectrons, one or more pickup electrodes, and a fragmentation device,
• controlling the ELIT to measure a time domain image current of the oscillating ions from ion injection to a total acquisition time, Tacq1, using the one or more pickup electrodes and to perform position-dependent fragmentation of the oscillating ions within Tacq1 at one or both turning points of the oscillating ions adding product ions to the oscillating ions using the fragmentation device using the processor, wherein the fragmentation is performed at a delay time, tact, relative to the ion injection that is increased by a time increment, Δtact, in each subsequent acquisition, n+1, making the fragmentation of the oscillating ions dependent on their position, and
• storing the measured time domain image current as a row or column n of a two-dimensional matrix in a memory device.

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 controlling a mass spectrometer to simultaneously measure precursor and product ion data, 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 a storage and analysis module;
• and
• controlling ion transfer optics and an ELIT to perform a total number of acquisitions, N, using the control module and, for each acquisition, n, of the N acquisitions,
• controlling the ion transfer optics to inject ions from the ion beam into the ELIT causing the ions to oscillate axially between two electric fields produced by two the sets of reflectrons using the control module, wherein the ion beam is produced by an ion source configured to ionize a sample and wherein the ELIT includes the two sets of reflectrons, one or more pickup electrodes, and a fragmentation device,
• controlling the ELIT to measure a time domain image current of the oscillating ions from ion injection to a total acquisition time, Tacq1, using the one or more pickup electrodes and to perform position-dependent fragmentation of the oscillating ions within Tacq1 at one or both turning points of the oscillating ions adding product ions to the oscillating ions using the fragmentation device using the control module, wherein the fragmentation is performed at a delay time, tact, relative to the ion injection that is increased by a time increment, Δt, in each subsequent acquisition, n+1, making the fragmentation of the oscillating ions dependent on their position, and
• storing the measured time domain image current as a row or column n of a two-dimensional matrix in a memory device using the storage and analysis module.