Mass Spectrometry in Systems Biology - Systems Biology: Networks, Models, and Applications - page 6

It is worth noting that for quadrupole filters unit resolution is used
rather that resolution. Unit resolution defines the ability of the quadru-
pole mass filter to resolve m / z signals that are 1 unit apart. Recent
instrument developments have increased quadrupole mass accuracy to
5 ppm and its resolution up to 5000 [5].
Ion trap instruments are electrical multipoles, formed by rods and
“doughnut”-shaped electrodes (toroidal arrangement) (figure 1.1c). The
RF electric field of an ion trap constrains the motion of ions in the XY
direction while end-cap electrodes constrain the ions in the Z direction.
Upon perturbation of the electric field, ions with increasing m / z values
are ejected from the ion trap toward the detector, in what became
known as mass-selective instability mode. As opposed to quadrupole
mass filter, in an ion trap all ions are stored except the ones with m / z
value matching the ejecting potential. Mass accuracy and unit resolu-
tion are similar in quadrupole mass filters, 300 ppm and 2000. However,
because of highly efficient use of all ions produced, ion traps are more
sensitive than quadrupole mass filters.
Ions can also be trapped in a mass analyzer by static high magnetic
fields. Ions trapped within a high magnetic field assume a cyclotronic
motion giving these mass analyzers their name, ion cyclotron reso-
nance (ICR) mass spectrometers (figure 1.1d). In ICR, the rotation
frequency of an ion in the magnetic field is proportional to its mass-to-
charge ratio. Mass analyzers and a detector are combined in ICR trap.
In a highly simplified view, ions move at a specific frequency in ICR
and consequently generate a current (image current) that is detected
over time by the detection plates (electrodes) of ICR cells. The recorded
signal is then transferred from time to frequency domain (Fourier
transform, FT) to obtain a mass spectrum, since ion frequency is pro-
portional to m / z . FT-ICR MS has high mass accuracy (1-2 ppm) and
high resolution (

100,000).
Mass-to-charge ratios can be resolved and measured accurately but
they do not describe the covalent structure of biomolecules. Mass spec-
trometers were developed to measure both molecular weight and
covalent structure using the following sequence of events: (i) mass
measurement of molecular ions, (ii) fragmentation reaction, and (iii) mass
measurement of fragments of molecular ions. This sequence of events
describes the operation of tandem mass spectrometer (MS/MS) that is
commonly used in the structural analysis of biomolecules.
One example of a tandem mass spectrometer is the serial arrange-
ment of two quadrupole mass filters interspaced by a collision cell, also
known as a triple quadrupole system (figure 1.2a). Mass measurement
in the first mass filter is followed by collision-activated dissociation
(CAD) with noble gases such as argon or helium and analysis of the
fragment ions in the second mass analyzer. These devices can also be
used for highly specific and accurate quantitation of ions by monitoring

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