Method for top down proteomics using ExD and PTR

A method for reducing the charge of at least two product ions in order to move the mass-to-charge ratio (m/z) values of the at least two product ions above a threshold m/z value and decrease overlap among the m/z values of the at least two product ions before mass analysis, comprising:

• instructing a reagent source device to supply charge reducing reagent using a processor;
• instructing a dissociation device to receive a precursor ion and fragment the precursor ion using the processor, producing a plurality of product ions in the dissociation device;
• instructing the dissociation device to receive the charge reducing reagent from the reagent source device using the processor;
• instructing the dissociation device to apply an alternating current (AC) voltage and a direct current (DC) voltage to one or more electrodes of the dissociation device that creates a pseudopotential in an axial direction to trap product ions of the plurality of product ions with m/z values below a threshold m/z in the dissociation device and to, in turn, cause the trapped product ions to be charge reduced by the received charge reducing reagent so that m/z values of at least two product ions of the trapped product ions increase to m/z values above the threshold m/z using the processor;
• and
• instructing the dissociation device to apply the DC voltage to the one or more electrodes relative to a DC voltage applied to electrodes of a next device positioned after the dissociation device that causes the at least two product ions with m/z values increased above the threshold m/z to be continuously transmitted to the next device 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 reducing the charge of at least two product ions in order to move the mass-to-charge ratio (m/z) values of the at least two product ions above a threshold m/z value and decrease overlap among the m/z values of the at least two product ions before mass analysis, 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;
• instructing a reagent source device to supply charge reducing reagent using the control module;
• instructing a dissociation device to receive a precursor ion and fragment the precursor ion using the control module, producing a plurality of product ions in the dissociation;
• instructing the dissociation device to receive the charge reducing reagent from the reagent source device using the control module;
• instructing the dissociation device to apply an alternating current (AC) voltage and a direct current (DC) voltage to one or more electrodes of the dissociation device that creates a pseudopotential in an axial direction to trap product ions of the plurality of product ions with m/z values below a threshold m/z in the dissociation device and to, in turn, cause the trapped product ions to be charge reduced by the received charge reducing reagent so that m/z values of at least two product ions of the trapped product ions increase to m/z values above the threshold m/z using the control module;
• and
• instructing the dissociation device to apply the DC voltage to the one or more electrodes relative to a DC voltage applied to electrodes of a next device positioned after the dissociation device that causes the at least two product ions with m/z values increased above the threshold m/z to be continuously transmitted to the next device using the control module.