Mass Spectrometry in Systems Biology - Systems Biology: Networks, Models, and Applications - page 2

systematically analyze compounds in all three major subdomains of
systems biology: genomics, proteomics, and metabolomics (including
its branches lipidomics, glycomics, etc.). Proteomics (analysis and char-
acterization of large collections of proteins) analysis by MS is by far the
most advanced [6].
In this chapter, we will outline the basic principles of MS. We will
focus on analytical contribution of MS to proteomics and to a lesser
extent to lipidomics. State-of-the-art technology is available for pro-
teomics and is emerging for lipidomics. Proteomics and lipidomics
experiments employ different facets of analytical methods that are
coupled with or based on MS. Integration of large-scale MS data for
proteomics, particularly with mRNA expression profiles generated
from microarray studies, and from some lipidomics studies, will be
highlighted. Finally, we will see the promise of MS for systems biology.
BASIC PRINCIPLES OF MASS SPECTROMETRY
Mass spectrometers are composed of three major units: an ion source,
a mass analyzer, and a detector. Together, these three units allow mass
spectrometers to measure a fundamental physicochemical property of
a molecule: the mass-to-charge ( m / z ) ratio of its gas-phase ions.
Ionization
Biological sample introduction to a mass spectrometer requires pro-
duction of volatile, gas-phase ions of biomolecules. Biomolecular MS
relies mostly on two processes for robust and reasonably unbiased
ionization of bioanalytes: electrospray ionizaton (ESI) and matrix-
assisted laser desorption ionization (MALDI). Underscoring the
importance of soft ionization processes, discovery of ESI and MALDI
was recognized with the Nobel Prize for Chemistry in 2002 [7,8].
In ESI, a high electric field (2-5 kV) applied between the tip of the
capillary (anode) and the inlet of the mass spectrometer (cathode) forms
electrically charged liquid droplets that are then further evaporated.
Gas-phase ions are then transferred to the mass spectrometer down both
a potential and a pressure gradient. A significant advantage of ESI is the
ease of interfacing separation techniques with mass spectrometers.
In MALDI, biomolecules are cocrystallized with an energy-absorbent
substance (matrix) [9]. Matrix molecules rapidly absorb the energy of
irradiation (from laser pulses) and promote vaporization of matrix-
analyte complexes followed by ionization of the analytes. For both
MALDI and ESI, the efficiency of the ionization process is an important
determinant of the sensitivity of detection, that is, the response of the
instrument for a given concentration of analyte.
Peptides are readily ionized in acidic buffers. Depending on the
polarity of the molecule one could use either positive or negative