Proteome analysis/annotation

Knowledge of protein primary sequence, quantities, posttranslational modifications (PTMs), structures, protein-protein (P-P) interactions, cellular spatial relationships, and functions are seven important attributes (see Table 4.2) needed for comprehensive protein expression analysis. It is this multifold and complex nature of protein attributes that has spawned the development of so different many proteomic technologies. Some of these challenges in proteomic analysis include defining the identities and quantities of an entire proteome in a particular spatial location (i.e., serum, liver mitochondria, brain), the existence of multiple protein forms and complexes, the evolving structural and functional annotations of the human and rodent... 

Ahmed, F. E. 2009. Utility of mass spectrometry for proteome analysis Part II. Ion-activation methods, statistics, bioinformatics and annotation. Expert Rev. Proteomics 6(2) 171-97. 

The current situation in bioinformatics is characterized by an avalanche of DNA sequences from the human genome project and similar programs and, consequently, an exponential increase in DNA sequences but only a linear increase in protein 3D structures. While multitudes of putative genes have been annotated, up to 90% of all known DNA sequences have no assigned, i.e., experimentally proven, function. From this situation arise the need for interpretation of DNA sequences by information technology, and moreover, analysis of functional genomics and proteomics (see Chapter 15). 

Figure 1 Schematic illustration of the proteomics process comprising the utilization of both gel-base and liquid-phase separations interphased to mass spectrometry analysis followed by database search mining, annotation, and a final link to the functional role of proteins.

Tebbe, A., Klein, C., Schmidt, A., Bisle, B., Konstandinidis, K., Scheffer, B., Lottspeich, F., Siedler, F., Pfeiffer, F. and Oesterhelt, D. (2005) Analysis of the cytosolic proteome of halobac-terium salinamm - implications for genome annotation and differential expression. Proceedings of the 53rd ASMS Conference on Mass Spectrometry and Allied Topics, San Antonio, TX, June5-June9, 2005. 

Computational proteomics refers to the large-scale generation and analysis of 3D protein structural information. Accurate prediction of protein contact maps is the beginning and essential step for computational proteomics. The major resource for computational proteomics is the currently available information on protein and nucleic acid structures. The 3D-GENOM1CS (www.sbg.bio.ic.au.uk/3dgenomics/) and PDB (http // www.rcsb.org/pdb/), and other databases provide a broad range of structural and functional annotations for proteins from sequenced genomes and protein 3D structures, which make a solid foundation for computational proteomics. 

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