Proteome Analysis Database

Proteome refers to protein complement expressed by a genome. Thus proteomics concerns with the analysis of complete complements of proteins. It is the study of proteins that are encoded by the genes of a cell or an organism. Such study includes determination of protein expression, identification and quantification of proteins as well as characterization of protein structures, functions and interactions. The functional classification of proteins in genomes (i.e., proteomes) can be accessed from the Proteome Analysis Database at http //ebi.ac.uk/proteome/ (Apweiler et ah, 2001). 

Mulder, N., Phan, I., Servant, F., Apweiler, R. (2003). The Proteome Analysis Database a tool for the in silico analysis of whole proteomes. Nucleic Acids Res. 31, 414417. 

A variety of protein/DNA databases, such as GenBank, EMBL, NCBI, GenPept, Swiss-Prot, TrEMBL, PIR, OWL, IPI, and dbEST, are maintained by independent research groups for use by the public for proteome analysis. Databases have links to other databases and also provide vital information related to the identified proteins such as functions, any PTMs, domain and sites, 3D structures, homology to other proteins, associated diseases, sequence conflicts, and variants. 

Figure 1. (a) Overview of the progress and objectives of proteomics and (b) the structure of PADB, a proteomic analysis database. 

Simpson RJ et al. Proteomic analysis of the human colon carcinoma cell line (LIM 1215] development of a membrane protein database. Electrophoresis 2000 21 1707-1732. 

Journet A et al. Towards a human repertoire of monocytic lysosomal proteins. Electrophoresis 2000 21 3411-3419. Soskic V et al. Functional proteomics analysis of signal transduction pathways of the platelet-derived growth factor beta receptor. Biochemistry 1999 38 1757-1764. Thiede B et al. A two dimensional electrophoresis database of a human Jurkat T-cell line. Electrophoresis 2000 21 2713-2720. 

MS instruments measure the mass-to-charge ratio (m/z) values of the smallest of molecules very accurately. In addition, the development of translated genomic databases and specialized software algorithms that rapidly search MS data against theoretical spectra of known or predicted proteins within databases is an important component that greatly facilitated the emergence of mass spectrometry-based proteomics as a key approach for large-scale proteomic analysis.15... 

The limitations of genomic analysis are being addressed by proteomic analysis. DNA sequence analysis has helped to create protein product libraries and relational databases that hold promise to... 

RA VanBogelen, KZ Abshire, B Moldover, ER Olson, FC Neidhardt. Escherichia coli proteome analysis using the gene-protein database. Electrophoresis 18 1243-1251, 1997. 

Bioinformatics The use of information technology to analyze data obtained from proteomic analysis. An example is the use of databases such as SWISSPROT to identify proteins from sequence information determined by the mass spec-trometric analysis of peptides. See Wang, J.T.L., Data Mining in Bioinformatics, Springer, London, 2005 Lesk, A.M., Introduction to Bioinformatics, Oxford University Press, New York, 2005 Englbrecht, C.C. and Facius, A., Bioinformatics challenges in proteomics. Comb. Chem. High... 

Mass spectrometry has become a major player in proteome analysis because of its integration with high-resolution separation techniques and protein databases and its inherent high sensitivity, high structure specificity, high-mass capability, and opportunity for automation. Short analysis times and straightforward sample preparation steps are the other advantages of mass spectrometry-based proteomics. 

A general outline of the bottom-up mass spectrometry approach for proteome analysis is presented in Figure 3. In general, the mass spectrometry is performed at the peptide level after digesting the protein to obtain the molecular mass and amino acid sequence-specific ions, which are correlated with similar information in the protein or nucleotide database.7 16 Based upon these measurements, the following approaches have evolved. 

Appel, R.D., A. Bairoch and D.F. Hochstrasser. 2D databases on the World Wide Web. In 2D Proteome Analysis Protocols Methods in Molecular Biology, edited by AJ. Link, Totowa, NJ, Humana Press, pp. 383-391, 1999. 

---