Mass Spectrometry in Systems Biology - Systems Biology: Networks, Models, and Applications - page 9

A simple yet powerful setup is the linear ion trap (LIT) as a stand-
alone instrument (figure 1.2d). The end-cap electrodes control the
injection of ions into the linear ion trap and when ions are ejected
from the trap, they exit to detectors on both sides of the trap. A benefit
to this configuration is that there is no loss of ions during detection.
Linear ion traps are fast-scanning instruments and can acquire at
a rate of 5 spectra/s [14]. MS/MS is performed in the same physical
location in the following sequence: isolate the ion of interest, perform
CAD (fragmentation), and measure the products of the reaction. In
general, ion traps can perform this cycle (isolation, fragmentation, and
mass analysis) for many ( n ) stages (MS n ).
Fourier transform mass spectrometry (FTMS) is unparalleled in its
mass measurement accuracy and resolution, but is not very effective at
performing multistage mass spectrometry experiments. However,
hybrid FTMS instruments that combine a linear ion trap as the first
mass analyzer for FTMS allows MS/MS experiments to be performed
at high scanning speed (in linear ion trap) in advance of high mass
accuracy and resolution measurements (figure 1.2e).
Operation of mass spectrometers is directed by an instrument con-
trol system. For example, the instrument control system monitors mass
analyzers, detectors, and a portion of ion source under proper vacuum
conditions. Besides maintaining operational parameters, the software
for instrument control is the interface for designing unique mass
spectrometry experiments. One such example is data-dependent acqui-
sition, illustrated in figure 1.3. The figure legend contains detailed
information about the instrument routine.
Most of the current large-scale analysis of peptides is based on data-
dependent acquisition performed under the control of a computer,
where measurement of m / z of biomolecules (full scan mass spectrum)
is followed by tandem mass spectra of the most abundant ions from
full scan MS. However, beside data-dependent acquisition, more spe-
cialized experiments (i.e., precursor ion scan, product ion scan, neutral
loss ion scan, presented in refs. [15] and [16]) describe fine structural
properties of biomolecules. For example, precursor ion scanning has
been used for profiling classes of lipids [10].
Analysis of biological samples by large-scale MS experiments repre-
sents a compromise between the acquisition rate of the instrument
(scan speed) and how informative the collected data are. To summa-
rize, we extract information from an experiment only under proper
sensitivity conditions (see previous section) and appropriate resolution
and mass accuracy. Moreover, in analyzing a mixture of compounds,
fragmentation spectra are necessary for complete identification. When
designing an experiment for comprehensive characterization of a bio-
logical entity, the choice of one instrument over another should take
into consideration how any of the above factors will influence the