The objective of proteomics is the systematic analysis of the proteins expressed by a cell, tissue or organism. It is expected that such analyses will define comprehensive molecular signatures of tissues, cells and body fluids in health and disease. These signatures will impact a wide range of biological and clinical research questions, such as the systematic study of biological processes and the discovery of molecular clinical markers for detection, diagnosis and assessment of treatment outcome. The application of proteomics technology has proven particularly beneficial in cases in which differences between the proteomes (or fractions thereof) isolated from cells at different states have been analyzed. The detection of differences between proteomes implies that the measurements include accurate quantification. A number of new methods based on stable isotope tagging and tandem mass spectrometry have been developed that now support robust quantitative proteome analysis.
These methods have in common that they are intended to collect high quality data at high throughput. In this presentation, we will discuss recent advances in quantitative proteomics technology, its current status and limitations. Specific emphasis will be placed on the challenges of collecting, analyzing, storing and mining large proteomic datasets. Finally, we will discuss new experimental approaches that have the potential to significantly improve the performance and sample throughput of mass spectrometry based proteomics technology.
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