Instrumentation for LC-MS/MS in Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 49

their voltage is not changing and ions are oscillated only radially.
The main advantages of linear ion traps over 3D traps are their
more efficient ion trapping and larger ion capacity, allowing them
to produce spectra with higher signal-to-noise and better dynamic
range ( 11 ) .
The equations describing the stability of ions inside a
quadrupole ion trap are not simple. However, commercial
quadrupole ion trap instruments are operated in a way that main-
tains stability in the axial direction; so manipulation of stability
in the radial direction, by altering a parameter known as the q z ,
is used for determining whether an ion is trapped or not. The
parameter q z is defined by a combination of the m / z of the ion,
the ion trap radius, and the frequency and amplitude of the RF
voltage applied. Scans are performed by changing the amplitude
of the RF voltage to sequentially eject ions radially, normally from
lowtohighmass( 12 ) . As ions are ejected, they are detected, and
by correlating the time of detection to the RF amplitude, it is
possible to determine their mass-to-charge ratio ( m / z ).
Ions of a given m / z in the quadrupole ion trap will be mov-
ing in a motion at a certain frequency. By applying an AC voltage
on the end-cap electrodes at the same frequency as this motion,
it is possible to resonantly excite ions of that m / z . These ions
collide with gas molecules in the ion trap and can cause frag-
mentation through collision-induced dissociation (CID). Unfor-
tunately, low-mass ions (below about one-third of the precursor
m / z ) formed from CID analysis will have a q z value too high
to be trapped, meaning the low-mass region of the fragmenta-
tion spectrum is missing. By resonantly exciting for a very short
period of time, it is possible to still trap a few low-mass ions (a
technique called pulsed Q dissociation or PQD). However, this
compromises the fragmentation efficiency. By applying a higher
amount of resonant excitation, it is possible to eject ions from
the trap without fragmentation, and this provides an alternative
method for isolating a particular ion to scanning ions out at the
extremes of the q z stability range.
Quadrupole ion traps are the most common type of ion trap
in use, and almost invariably if someone states that they are using
an ion trap mass spectrometer, they mean a quadrupole ion trap
instrument. The instruments are known for their high sensitivity.
Their resolving power (ability to distinguish between components
of similar masses) is dependent on the rate at which they scan the
mass range. However, as one cannot detect new ions until the
previous ions have been scanned/ejected out of the trap, fast scan
rates are typically employed to maximize sensitivity and speed. As
a result, ion trap data are typically of low resolution and relatively
poor mass accuracy.
If too many ions are isolated in any type of ion trap, the charge
density causes ions to interact with each other (referred to as