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The Proteome of a living organism is the collection of proteins that are present in that organism. All these proteins are encoded based on the genome of an organism, but undergo substantial differentiation (Post Translational Modifications or PTMs) after translation. In the human DNA there are about 30.000 genes, but the number of human proteins is estimated to be around 300.000 different types.

In addition to the huge complexity of the proteome composition, proteins levels vary over a range of 109 orders of magnitude! Human plasma contains high abundant proteins such as Albumin (55% in plasma) and Immunoglobulins, but the proteins of interest (e.g. Interleukins or tissue leakage markers) are low abundant and a million to a billion times lower in concentration. On the human scale, this abundance difference relates to searching for a small blade of grass in the complete Amazon rain forest.

The structure, modifications and levels of these proteins reflect the physiological state of an organism. Proteomics is the field of research that has set out to map all the content and dynamics in the proteome; especially the human proteome.

Proteomics can be divided roughly into four areas which can blend into each other:

  • Targeted proteomics
  • Structural proteomics
  • Biomarker validation
  • Biomarker discovery

A large portion of the effort in Proteomics research is done in the area of biomarker research. Scientists are comparing healthy states and disease states of an organism to identify differences in protein expression. Depending on the disease a protein can be found to be up- or down regulated. When this difference in expression is observed, a potential biomarker has been discovered.

The next step would be to verify the validity of a potential biomarker by scanning a larger sample pool specifically for that marker. This typically involves two stages in biomarker research:

  • The discovery phase, comprehensive approach analyzing few samples in depth
  • The validation phase, targeted approach analyzing many sample for the presence of specific proteins

Not all proteomics research is related to biomarkers; unraveling a disease pathway requires a more targeted approach. Post translational modifications play a critical role in cellular processes and usually involve the addition of a small molecule to the protein that is critical to the functionality of the protein. Fortunately the PTM’s often introduce a special feature that can be exploited in the separation and detection phase.

For practical reasons > 90% of proteomics research is centered around peptide detection (so called Bottom-Up approaches), but preferably the digestion step is excluded from the experiment. More and more effort in proteomics is being spent on intact proteins analysis or so called Top-Down approaches.

Anderson and Anderson – Mol Cell Prot - 2002 - 11 - 845-869