Proteomics protein 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. 

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

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). 

Wilkins MR, Williams KL, Appel RD, Hochstrasser DF (1997) Proteome research new frontiers in functional genomics. Springer Verlag, Berlin Heidelberg Yates JR, Speicher S, Griffin PR, Hunkapiller T (1993) Peptide mass maps A highly informative approach to protein identification. Anal Biochem 214 397—408 Yates JR, Eng JK, McCormack AL, Schieltz D (1995) Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database. Analytical Chemistry 67 1426-1436. 

Figure 1 5 MALDI spectrum from a 2-D gel spot excised from a human proteomic study in which the corresponding spectrum of the cathepsin D precursor could be identified after using SMEC micropreparation sample preparation followed by elution and spotting onto the MALDI target plate and MALDI analysis. The peptide mass fingerprinting revealed the identity of the protein using the Mascot bioinformatic software and the Swissprot protein database. The ( ) indicates the peptide masses corresponding to the cathepsin D precursor, and (T) the trypsin peptide fragments that were used for internal mass calibration.

There are four gel protein databases of cardiac proteins, established by three independent groups, that can be accessed via the World Wide Web (Table 16.1). These databases facilitate proteomic research into heart diseases containing information on several hundred cardiac proteins that have been identified by protein chemical methods. They all conform to the rules for federated 2-D protein databases (Appel et al., 1996). In addition, 2-D protein databases for other mammals, such as the mouse, rat (li et al., 1999), dog (Dimn et al., 1997), pig and cow, are also under construction to support work on animal models of heart disease and heart failure. 

HPRD www.hprd.org/ Licence for commercial user Human proteome annotation database including 33,000 manually curated Human protein interaction Peri et al. (2003)... 

Sheng S, Chen D, van Eyk JE (2006) Multidimensional liquid chromatography separadon of intact proteins by chromatographic focusing and reversed phase of the human serum proteome Optimizadon and protein database. Mol Cell Proteomics 5 26-34. 

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 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. 

This Section briefly describes the data resources available and relevant for researchers working in proteomics. The databases can be classified according to the type of information provided, i.e. protein sequence, nucleotide sequence, pattern/profile, 2-DE, 3-D structure, PTM, genomic, and metabolic. A more extensive description and list has been published by Bairoch [55], A reasonably exhaustive and constantly updated list of databases can also be found at http //www.expasy.org/alinks.html. Here we focus on sequence databases, protein domain databases, 2-D PAGE, and PTM databases. 

The establishment of species- and tissue-specific protein databases provides a foundation for proteomics studies of diseases. Continual development will lead to functional proteomics studies, in which identification of protein modification in conjunction with functional data from established biochemical and physiological methods enables the examination of interplay between changes in a proteome and the progression of diseases. Recently, many investigations provided direct evidence for PTM in the pathophysiological progression of many diseases like diabetes, Alzheimer s diseases (AD), atherosclerosis, and oncogenesis. 

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