Instrumentation for LC-MS/MS in Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 53

and high-specificity monitoring of a set of components ( 25 ) , and
this approach has great applicability for monitoring biomarkers in
complex biological fluids ( 26 ) .

The Q-trap is identical to a triple quadrupole instrument except
that the final quadrupole has been replaced by a quadrupole ion
trap. This dramatically improves the sensitivity of the instrument
for scanning mass ranges and makes the instrument more suitable
for analyzing peptide fragmentation spectra. The final ion trap
can also be used as a quadrupole; so SRM studies can also be
performed using this instrument ( 26 , 27 ) .

3.2.2.Q-Traps

The basis of mass analysis by time of flight (TOF) resides in the
fact that when ions are accelerated with the same kinetic energy,
ions of higher m / z will have a lower velocity. Hence, by mea-
suring the time ions take to travel along a flight path to a detec-
tor, it is possible to determine their m / z . Most TOF mass spec-
trometers, rather than having a simple linear flight path to the
detector, employ an ion mirror or a reflectron that “bounces”
the ions back to a detector toward the other end of the flight
tube ( 28 ) . This is a mechanism that allows partial compensa-
tion for any variation in initial kinetic energy that ions may have
had; if two ions of the same m / z had slightly different initial
kinetic energies, then the one with higher kinetic energy will
have slightly higher velocity and so will penetrate further into
the ion reflectron and take more time to be reflected. By posi-
tioning the detector at the correct focus point, the two ions of
slightly different initial kinetic energies but same m / z will be
detected at the same time. The use of a reflectron improves the
resolution and mass accuracy of TOF mass spectrometers, giv-
ing performance in between a quadrupole ion trap and an orbi-
trap or FT-ICR mass spectrometer. In a TOF analyzer, all accel-
erated ions are measured. Hence, because of their short duty
cycle, TOF instruments are relatively sensitive when compared to
quadrupoles.
QqTOF instruments employ a first quadrupole for precursor
isolation and a second as a fragmentation chamber in the same
way as triple quadrupole and Q-trap instruments. However, the
final analyzer is a TOF with a flight path orthogonal to the axis
of the quadrupoles ( 29 ) , as shown in Fig. 3.3 . For TOF analysis,
ions need to start with no initial kinetic energy, then a packet of
ions are accelerated together, and flight times are measured. Ions
passing through the quadrupoles in a QqTOF have kinetic energy
in the plane of the quadrupole axes but none in the orthogonal
direction and so are suitable for TOF measurement perpendicular
to their flight path.
QqTOF instruments are good compromise instruments
between sensitivity, mass accuracy, and resolution; they are more

3.2.3.QqTOF