Instrumentation for LC-MS/MS in Proteomics - LC-MS/MS in Proteomics: Methods and Applications - page 55

CID spectra to be acquired (although they must be measured in
the orbitrap) ( 30 ) . It is also used as a transmission cell for intro-
duction of anions for electron transfer dissociation (ETD) frag-
mentation ( 31 ) (seebelow).

Fig. 3.4. Schematic of an LTQ-Orbitrap XL enabled with ETD. Analyte ions are introduced
on the left of the instrument and pass through into the linear quadrupole ion trap. Ions
can be measured in the linear trap at high sensitivity or passed out of the trap and
diverted into the orbitrap through the C-trap for high mass accuracy and resolution
measurement. For ETD analysis, anions are produced in the CI source at the right of
the instrument and are passed through the HCD cell and C-trap to the linear ion trap,
where ETD fragmentation occurs. Yet again, ions can then be measured in either the
linear ion trap or orbitrap. Quadrupole (rather than quadrupole ion trap) fragmentation
analysis can be performed in the HCD cell but can be measured only in the orbitrap.

Interfacing a quadrupole ion trap with an FT-ICR gives very sim-
ilar functionality to an LTQ-Orbitrap, with the ability to measure
ions either at high sensitivity or with high mass accuracy ( 32 ) .
FT-ICR can produce higher resolution measurement than can an
orbitrap, but for proteomic applications, both have more reso-
lution than strictly required. The advantages of the orbitrap are
better dynamic range and sensitivity; the transfer distance between
quadrupole trap and orbitrap is significantly shorter than into the
cell inside an FT-ICR magnet; so there is less sample loss dur-
ing ion transfer. However, the FT instrument does provide the
opportunity to employ different fragmentation mechanisms.

3.2.5.Quadrupole Ion
Trap-FT

CID is the major fragmentation approach employed in mass spec-
trometers but is not the only approach employed for proteomic
studies, and particularly the use of ETD is likely to increase in the
near future. Also, CID in a quadrupole ion trap produces slightly
different fragmentation to CID performed in a quadrupole and
the two methods are found to be complementary (see below).

3.3.Fragmentation
Alternatives

CID fragmentation in a quadrupole ion trap is produced by reso-
nant excitation of a specific m / z . Hence, once the component has
been fragmented, its products are not further excited. This means
that the majority of the fragments observed are the products of

3.3.1.CID
inaQuadrupole IonTrap
vs inaQuadrupole