Multiplexed precursor isolation for mass spectrometry

A method for identifying precursor ions of product ions from combined product ion spectra produced by a tandem mass spectrometer that includes a mass filter that performs multiplexed precursor ion selection, comprising:

• selecting N precursor ions using a processor;
• creating N groups of the N precursor ions using the processor, wherein each of the N groups has N−1 precursor ions of the N precursor ions and wherein a different precursor ion of the N precursor ions is not included in each of the N groups;
• instructing a tandem mass spectrometer to perform multiplexed precursor ion selection on a continuous beam of ions provided by an ion source for each of the N groups, fragment each of the N−1 precursor ions selected in each of the N groups, and measure the intensities of the product ions produced by each of the N groups using the processor, producing N product ion spectra;
• plotting a heat map for each of the N product ion spectra using the processor, producing N heat maps;
• combining the N product ion spectra into a combined product ion spectrum using the processor, and
• identifying a precursor ion of a peak in the combined product ion spectrum by finding a heat map of the N heat maps that does not have data for the mass of the peak and determining that a precursor ion of the N precursor ions that is not included in a group that produced the heat map is the identified precursor ion using the processor.

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 identifying precursor ions of product ions from combined product ion spectra produced by a tandem mass spectrometer that includes a mass filter that performs multiplexed precursor ion selection, 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 identification module;
• selecting N precursor ions using the control module;
• creating N groups of the N precursor ions using the control module, wherein each of the N groups has N−1 precursor ions of the N precursor ions and wherein a different precursor ion of the N precursor ions is not included in each of the N groups;
• instructing a tandem mass spectrometer to perform multiplexed precursor ion selection on a continuous beam of ions provided by an ion source for each of the N groups, fragment each of the N−1 precursor ions selected in each of the N groups, and measure the intensities of the product ions produced by each of the N groups using the control module, producing N product ion spectra;
• plotting a heat map for each of the N product ion spectra using the identification module, producing N heat maps;
• combining the N product ion spectra into a combined product ion spectrum using the identification module, and
• identifying a precursor ion of a peak in the combined product ion spectrum by finding a heat map of the N heat maps that does not have data for the mass of the peak and determining that a precursor ion of the N precursor ions that is not included in a group that produced the heat map is the identified precursor ion using the identification module.