Genome/proteome databases

Top-down proteomics [1] is the identification and characterization of a mature, intact protein (or proteins) using primarily mass spectrometry (MS)-based techniques and the sequence information contained in genomic/proteomic databases. Unhke bottom-up proteomics [2-4], where a protein (or proteins) is digested into peptides prior to MS or tandem mass spectrometry (MS/MS) analysis [3,4], the top-down approach involves measuring the molecular weight (MW) of the intact, mature protein with its associated posttranslational modifications (PTMs) if any. The intact protein ion is then fragmented in the gas phase in order to determine its amino acid sequence as well as the location and identification of PTMs. From its earliest development, top-down proteomics has been primarily the domain of electrospray ionization (ESI) [5] (which generates mul-... 

This is a reflection of the increasing knowledge of the complexity of in viva systems, and also the current powerful computational resources to capture, analyze, interpret and model those systems. In view of this complexity, not only the development of genomics, proteomics and metabonomics databases, but also the development of systems biology methods helps us to understand the underlying mechanisms in any given ADME process [80]. 

Gromov, P.S., Ostergaard, M., Gromova, I., Celis, J.E. (2002). Human proteomic databases, a powerful resource for functional genomics in health and disease. Prog. Biophys. Mol. Biol., 80, 3-22. 

Sources for specific omics studies are also available. For instance, tools such as the RNA-Seq Atlas [17], Human Protein Atlas (HPA) [18], and the Human Metabolome Database (HMDB) [19] are useful for systemic genomic, proteomic, and metabolo-mics studies of human beings. LIPID Metabolites and Pathways Strategy (LIPID MAPS) [20] is a lipidomics gateway, an integrative platform for studies in lipid biology. More resources and updated links can be found at the Biomarkers portal (see Table 1). 

The IntegrS portal (http //ebi.ac.uk/integr8) offers an overview of information about organism with completely sequenced genomes, statistical analysis of their genomes/ proteomes individually and comparatively. The database is build on three main sources (Kersey et al, 2005) ... 

Danish Centre for Human Genome Research http //biobase.dk/ cgi-bin/celis/ Danish Centre for Human Genome Research, University of Aarhus 2DE proteome database of human (primary keratinocytes, epithelial, hematopoietic, mesenchymal, hematopoietic, tumors, urothelium, amnion fluid, serum, urine, proteasomes, ribosomes, phosphorylations) and mpuse (epithelial and new bom) proteomes Free access via the internet... 

Immunomics offers an excellent example for application of the systems biology and modern genomics/proteomics technology. Immunomics comprises a fruitful combination of modern molecular immunology, animal modeling, omics technologies, and application of ever-increasing immune databases. 

The revolutionary development of chemical and functional omics approaches (genomics, proteomics, lipidomics, glycomics, etc.) has contributed to the emergence of database management, high-throughput... 

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