RF ion trap ion loading method

A mass spectrometer, comprising:

• a collision cell,
• a downstream analyzer ion trap,
• wherein the collision cell is configured to:
• receive first precursor ions and cause at least a portion of the first precursor ions into first ion fragments,
• release the first ion fragments into the collision cell,
• after releasing the first ion fragments, receive second precursor ions and cause fragmentation of at least a portion of the second precursor ions into second ion fragments, and
• release the second ion fragments into the collision cell,
• an RF voltage source configured to:
• apply a first voltage to the collision cell and a second voltage to the analyzer ion trap, wherein the first and second voltages preferentially confine high m/z ions,
• apply a third voltage to the collision cell and a fourth voltage to the analyzer ion trap after the first fragment ions have been released into the analyzer ion trap,
• wherein the third voltage and the fourth voltages preferentially confine low m/z ions,
• wherein the third and fourth voltages are lower than the first and second voltages respectively, and
• wherein the collision cell is configured to simultaneously contain high m/z ions and low m/z ions.

A method of processing ions in a mass spectrometer having a first ion trap and an analyzer ion trap positioned downstream of said first ion trap, each of said ion traps having a plurality of rods to at least one of which an RF voltage can be applied for radially confining at least a portion of ions within said trap, the method comprising:

• applying an RF voltage to said first ion trap so as to preferentially radially confine ions having m/z ratios above a threshold (“high m/z ions”),
• applying an RF voltage to said downstream analyzer ion trap so as to preferentially radially confine said high m/z ions,
• introducing a plurality of ions into said first ion trap,
• releasing at least a portion of said trapped ions from said first ion trap and introducing said released ions into said downstream analyzer ion trap,
• applying a pressure pulse to said downstream analyzer ion trap so as to expedite cooling of the ions received by said downstream analyzer ion trap,
• subsequently, reducing the RF voltages applied to said first ion trap and said downstream analyzer ion trap to a level suitable for radially confining ions having m/z ratios below said threshold (“low m/z ions”),
• introducing a plurality of ions into said first ion trap,
• releasing at least a portion of said ions from said first ion trap and introducing said released ions into said downstream analyzer ion trap such that the analyzer ion trap contains both the high m/z ions and the low m/z ions, and
• releasing the ions from said downstream analyzer ion trap using mass selective axial ejection.