The environment of a given organism determines the dynamics of gene expression, post-translational modifications of proteins and their interactions. Proteomics and genomics approaches now allow capturing these dynamics, which govern the life of an organism. Proteomics is devoted to the systematic study of proteins in order to derive a global perspective of the structures, functions and regulatory mechanisms in biological systems. The proteome represents the entire protein complement of a cell or a tissue a t a given time, in given environmental, physiological and/or pathological conditions. The dynamic nature of the proteome constitutes one of the major hurdles of proteomics analyses. Whereas the analysis of a single sample can potentially provide all the genetic information about an organism, a multitude of analyses in various conditions are necessary for proteome studies. Recent years have seen an intensive development in proteomics methodologies.
Among these, accurate mass and time (AMT) tag based proteomic is particularly promising to provide extensive proteome coverage with high throughput. An AMT tag database is established by using standard proteomics methods to identify peptides and their parent proteins. Identifications are then validated using accurate masses obtained by Fourier Transform Mass Spectrometry (FTMS) and Liquid Chromatography (LC) retention times. The AMT tag database obviates the need for MS/MS in all subsequent analyses, providing the basis for throughput improvements. We are getting involved in a large-scale effort to implement and develop AMT-tag based methods.
Our strategy includes new technological developments and biological applications. We plan to improve the method's quantitative ability, and to promote the use of alternative ion dissociation methods to study post-translational modifications. Initial applications include studies of the membrane from A. thaliana chloroplasts and of a mouse model of the graft vs host disease.
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