Ion trap MS permits structural information to be readily obtained (and sequence
information in the case of polypeptides). Not only can MS–MS analysis be carried out
but also due to the high efficiency of each stage, further fragmentation of selected ions
may be carried out to MS to the powern(MSn) (Fig. 9.8). The instrument still allows
accurate molecular mass determination to over 100 000 Da at greater than 0.01% mass
accuracy.
TheMSnprocedurein an ion trap involves ejecting all ions that are stored in the
trap, except those corresponding to the selectedm/zvalue. To performtandem MS
(MS^2 ) a collision gas is introduced (a low pressure of helium) andcollision-induced
dissociation(CID) occurs (Fig. 9.7). Thefragment ionsare then ejected in turn and the
fragment spectrumdetermined. The process can be repeated successively where all
the fragment ions stored in the trap except those fragment ions corresponding to
another selectedm/zvalue are ejected. This fragment ion can then be further frag-
mented to obtain more structural information, as illustrated for the example shown in
Fig. 9.8. This technique has a big advantage since no additional mass spectrometers(^500) m/z 600 700 800
(^300400500) m/z 600 700 800
Full MS
MS^2
MS^3 of 579.6
300 400 500 600 700 800
m/z
MS^3 of 561.2
300 400 500 600 700 800
m/z
638.39
561.21579.37597.30 653.40639.32654.45699.13720.99755.51767.20773.11785.07
615.32
637.33
615.32 (M+H)+ 637.33 (M+Na)+
412.32
561.19
579.20597.22
394.25430.27448.27
561.2
(M–3H 2 O)
597.6 (M–H 2 O)
579.6 (M–2H 2 O)
260.82293.08337.01393.41 449.02490.21560.17598.09650.14
394.24 448.3
319.24355.35 413.00 562.07
561.21
394.24
412.31
561.2
412.4
0 293.19294.97
319.10393.61
394.24 394.29
HO
HO
O
H
N N+
N+
SO 3 –
SO 3 –
OH
615.3 (M+H)+
HO
HO
O
H
N
OH
597.6 (M–H 2 O)
HO
HO
O
H
N
OH
448.3
O
H
N
394.29 (–3H 2 O)
Fig. 9.8Structural analysis, MSnin an ion trap. In this example, of a steroid-related compound, the structure
can be analysed when the (MþH)þions at 615.3 are selected to be retained in the ion trap. These ions are
subjected to collision-induced dissociation (CID) resulting in loss of the aliphatic sulphonate from the quaternary
ammonium group and partial loss of some hydroxyl groups in the tandem MS (MS^2 ) experiment. The major
fragment ions (561.2 and 579.6) are further selected for CID (MS^3 ) resulting in subsequent losses of more
hydroxyl groups from specific parts of the steroid ring.
363 9.3 Mass analysers