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Pharmaceutical proteomics: a journey from discovery and characterisation of targets to development of high-throughput assays

15 December 2013  •  Author(s): Joerg Reinders, Institute of Functional Genomics, University of Regensburg

Proteomics has evolved during the last few years from a time-intensive, cost-intensive and hard-to-reproduce technique in basic research to a versatile and reliable tool in various areas of pharmaceutical research. The exploding progress in mass-spectrometry-compatible protein and peptide-separation methods led to the development of new approaches particularly suited for monitoring a multitude of specific targets in highly complex matrices in a highly sensitive, specific and parallel fashion. These new technologies have caused a paradigm shift in proteomics from mostly gel-based, hypothesis-generating studies towards fast, cost-effective and mostly LC-MS-based assays. Therefore, proteomics emerges for pharmaceutical researchers aiming to identify and verify proteinaceous biomarkers as proteomics technology comes of age.

This mini-review highlights some of the recent technical developments that facilitate the use of proteomics as a tool for important steps in target protein identification, characterisation, biomarker discovery, validation and monitoring and discuss advantages and disadvantages of individual techniques.

Proteomics: from past to present

The term ‘proteome’ was coined as the entirety of all expressed proteins encoded in a genome1. In contrast to the genome which remains rather unchanged during an organisms` life and is the same for every cell, the proteome is not only altered by cell-type but is also highly dynamic due to various intrinsic and extrinsic factors that may affect it even within a few seconds. Proteomics therefore aims at a quantitative description of all proteins of a cell in parallel and their regulations by different stimuli. The necessity to identify and quantify thousands of proteins in parallel, typically from rather tiny available amounts of sample, poses a great challenge to analytical methods.

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