Biology Reference
In-Depth Information
of the 3D trap is that the trapping volume is small, so that deleteri-
ous ion-ion interactions, otherwise known as space-charge effects,
allow just a small number of ions to be trapped and analyzed effec-
tively. In addition, in MS/MS mode 3D ion traps typically have a
low mass cut-off which usually corresponds to about one-third of
the precursor ion mass. The fundamental limitations of the 3D trap
prompted researchers to investigate new trapping geometries, ulti-
mately leading to the development of the linear ion trap. The linear
ion trap (LIT), sometimes referred to as the two-dimensional (2D)
quadrupole ion trap, is such a recent development [
58
-
60
]. It
makes use of the basic structure of the quadrupole to confine ions
radially by a two-dimensional (2D) radio frequency (RF) field, and
axially by static electrical potentials applied to on-end electrodes.
One of the attractive features of linear ion traps for proteomic
experiments is that, in comparison to Paul traps, they have higher
injection efficiencies, higher ion storage capacities, and do not have
low mass cut-off. Linear traps have been combined with other mass
analyzers in hybrid configurations and used to isolate ions of
selected mass to charge ratios to perform tandem mass spectrom-
etry experiments (see below). ABSciex's QTRap™ system is a
hybrid triple quadrupole (Q
0
Q
1
Q
2
) linear ion-trap (LIT) (Q
3
)
mass spectrometer [
58
]. It can be operated in a conventional triple
quadrupole configuration with the traditional quadrupole scan-
ning modes: precursor ion, neutral loss, and multiple reaction
monitoring scans. In LIT mode, a pulse of ions passes through Q
1
operated as a conventional quadrupole mass filter to select the pre-
cursor ion of interest. The precursor ion is accelerated into the
pressurized Q
2
to promote fragmentation. The fragments and
residual precursor ion are then trap in the Q
3
linear ion trap. The
Q
3
RF voltage is then ramped to eject ions towards the detector. In
addition, enhanced MS survey and high sensitivity product ion
spectra are possible because while scanning out the ions from Q
3
,
ions can be accumulated in Q
0
and this gives a substantial increase
in signal intensity over normal operation mode.
A limitation for interfacing a continuous ion source, as ESI, to
a 3D trap is that ESI generates ions while the 3D trap is processing
other ions are not used, thereby limiting the duty cycle. The duty
cycle (Dc) of a 3D ion trap coupled directly to a continuous ion
source is Dc =
T
C
/(
T
C
+
T
A,3D
), where
T
C
is the ion trap fill time, and
T
A,3D
is the time for MS analysis in the 3D trap [
59
]. Injection effi-
ciencies are typically ≤ 5 % for externally created ions. Combining a
linear trap with a 3D trap, as in Thermo Fisher's linear trap quad-
rupole (LTQ) instruments, overcomes this limitation [
60
].
Accumulating ions in the linear trap while the 3D trap is processing
other ions increases the duty cycle to nearly 100 %. A TOF mass
spectrometer can also have a low-duty cycle when coupled with a
continuous ion source. Combining an ion trap with a TOF mass
analyzer also improves the duty cycle [
61
]. Thermo's LTQ FT
