Proteomics background

 

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, 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. Altogether, this leads to an enormous number of possible ‘proteoforms‘.

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.

 

Key technology: mass spectrometry

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 the late 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 & teaching material

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.

Book chapters on quantitative proteomics
» Karen A. Sap and Jeroen A. A. Demmers: “Labeling Methods in Mass Spectrometry Based Quantitative Proteomics” in Integrative Proteomics, ISBN 978-953-51-0070-6, DOI:10.5772/32489.
» Lennart van der Wal and Jeroen A. A. Demmers: “Quantitative Mass Spectrometry-based Proteomics” in Recent Advances in Proteomics, ISBN 978-953-51-2201-2, DOI:10.5772/61756.

Advanced reading material
» Steen and Mann (2004) The abc’s (and xyz’s) of peptide sequencing. Nat Rev Mol Cell Biol 5 (9): 699-711.
» Bantscheff et al. (2007) Quantitative mass spectrometry in proteomics: a critical review. Anal and Bioanal Chemistry 389 (4): 1017-1031.
» Ahrens et al. (2010) Generating and navigating proteome maps using mass spectrometry. Nature Reviews Molecular Cell Biology 11, 789-801.

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).

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