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191

The ion current measured during the AGC prescan is known as the AGC peak

area. The AGC peak area is proportional to the number of ions formed during the

prescan ionization. The AGC software uses the measured ion current as a

reference to optimize the ionization time for each scan as a function of analyte

concentration.

Scan Segment Setup Period

The prescan is followed by the first segment of the six scan segments. Each

segment can be divided into two parts: a setup period and a scanning period.

Each setup period can be subdivided into the following four stages:

First stage: The rf voltage is set to near 0V for 2 milliseconds. This setting

allows the rf voltage generator circuit to stabilize while clearing the trap cavity of

all ions.

Second stage: The rf voltage is set to, and stabilizes at, the storage voltage,

selected to store, or trap, all ions of interest in the ion trap cavity.

Third stage: First, the electron gate is turned ON. Energetic electrons from the

heated filament are accelerated into the ion trap, where they interact with sample

molecules and sample ions are formed. After the ionization period, the electron

gate is turned OFF, and additional electrons are prevented from entering the ion

trap.

The newly formed sample ions are then permitted to stabilize in their orbits at the

storage voltage. This stabilization period is referred to as the cool time. The

length of this period is fixed.

Fourth stage: The electron multiplier is made ready, and the rf voltage is

ramped quickly from the storage voltage to a value appropriate to begin the mass

scanning of the segment.

Mass Scanning

During mass analysis, the rf voltage is ramped from a low voltage to a higher

voltage.

The ion trap operates in the resonance ejection mode. In this mode, at low rf

voltage (for example, at the storage voltage) most ions have stable oscillations in

the ion trap cavity. However, as the rf voltage is increased, ions of progressively

greater mass-to-charge ratios become unstable and are ejected from the cavity.

The voltage at which an ion is ejected from the ion trap cavity is defined as its

resonance voltage. At a voltage below its resonance voltage, an ion travels in a

stable orbit, oscillating along all three axes. At or above its resonance voltage,

the trajectory of the ion becomes unstable. As the rf voltage increases above the

resonance voltage, the amplitude of the oscillation of the ion increases most

rapidly in the axial direction. As a result, when ions are no longer stable in the ion

trap cavity, they are ejected from the cavity in a tightly collimated beam upward

and downward. The ejection of ions of each mass-to-charge ratio occurs over a

very short time period. One half of the ions go up; these ions strike the top

endcap and are neutralized. The other half of the ions go down and pass through

the holes in the bottom endcap; many of these ions strike the electron multiplier

and are detected.

The rf voltage is ramped at a constant rate of approximately 5600 m/z per sec.

One complete scan at this fixed rate produces a microscan. Depending upon the

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