Background
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Proteomics
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Proteomics is loosely defined as the global analysis of proteins in a
protein complex, organelle, cell, tissue or complete organism. The term
‘proteomics’ was coined to make an analogy with genomics, the study of the
genes. Proteomics, however, is much more complicated than genomics, mostly
because while an organism's genome is rather constant, a proteome differs
from cell to cell and constantly changes through its biochemical
interactions with the genome and the environment. One organism has
radically different protein expression in different parts of its body,
different stages of its life cycle and different environmental
conditions.
First, the level of transcription of a gene gives only a rough estimate of
its level of expression into a protein. An mRNA produced in abundance may
be degraded rapidly or translated inefficiently, resulting in a small
amount of protein. Second, many proteins experience post-translational
modifications that profoundly affect their activities. For instance, a
protein may not be active until it becomes phosphorylated. Third, many
transcripts give rise to more than one protein, through alternative
splicing or alternative post-translational modifications. Finally, many
proteins form complexes with other proteins or RNA molecules, and only
function in the presence of these other molecules.
It is a widely accepted concept in biology nowadays that the far majority
of the proteins in a cell are assembled in larger complexes to exert their
function and one of our major goals to identify which proteins interact
with each other. This often gives important clues about the functions of
newly discovered proteins. Several methods are available to probe such
protein-protein interactions, most importantly immunoaffinity
chromatography under mild conditions followed by mass spectrometry to
identify the proteins.
Since proteins play a central role in the life of an organism, proteomics
is thought to be instrumental in finding novel ‘biomarkers’, such as
markers that indicate a particular disease.
Mass spectrometry
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A mass spectrometer determines the mass of a molecule by measuring the
mass-to-charge ratio (m/z) of its ion. Ions are generated by inducing
either the loss or gain of a charge from a neutral species. Once formed,
ions are electrostatically directed into a mass analyzer where they are
separated according to m/z and finally detected. The result of molecular
ionization, ion separation, and ion detection is a spectrum that can
provide molecular mass and even structural information. Over the past
decade, mass spectrometry has undergone tremendous technological
improvements allowing for its application to proteins, peptides,
carbohydrates, DNA, drugs, and many other biologically relevant molecules.
Due to ionization sources such as electrospray ionization (ESI) and
matrix-assisted laser desorption/ ionization (MALDI), mass spectrometry has
become an irreplaceable tool in the biological sciences.
According to John B. Fenn, the inventor of electrospray ionization for
biomolecules and the 2002 Nobel Laureate in Chemistry:
[...] mass spectrometry is the art of measuring atoms and molecules to
determine their molecular weight. Such mass or weight information is
sometimes sufficient, frequently necessary, and always useful in
determining the identity of a species. To practice this art one puts charge
on the molecules of interest, i.e., the analyte, then measures how the
trajectories of the resulting ions respond in vacuum to various
combinations of electric and magnetic fields. Clearly, the sine qua
non of such a method is the conversion of neutral analyte molecules
into ions. For small and simple species the ionization is readily carried
by gas-phase encounters between the neutral molecules and electrons,
photons, or other ions. In recent years, the efforts of many investigators
have led to new techniques for producing ions of species too large and
complex to be vaporized without substantial, even catastrophic,
decomposition.
Further reading
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For an introduction on the fundamental concepts of mass spectrometry, see
e.g. this book by Gary Siuzdak.
Reviews on mass spectrometry based proteomics:
» Ruedi Aebersold & Matthias Mann (2003) Mass
spectrometry based proteomics. Nature 422: 198-207.
» Bruno Domon & Ruedi Aebersold (2006) Mass spectrometry
and protein analysis. Science 312: 212-217.
A lot of information on proteomics and mass spectrometry can be found on
the websites of the American Society for Mass Spectrometry (ASMS) and the
Human Proteome Organization (HUPO).