Protein databases, gel

HSC-2DPAGE Harefield hospital 2D gel protein databases (HSC-2DPAGE)... 

AARHUS/GHENT- Human keratinocyte 2D gel protein database from Aarhus and... 

SWISS-2DPAGE Human 2D Gel Protein Database from University of Geneva (SWISS-2DPAGE)... 

Celis, J.E., Rasmusen, H.H., Madsen, P, et al. (1992). The human keratinocyte two-dimensional gel protein database, towards an integrated approach to the study of cell proliferation, differentiation, and skin diseases. Electrophoresis, 13(12), 893-959. 

M Perrot, F Sagliocco, T Mini, C Monribot, U Schneider, A Shevchenko, M Mann, P Jeno, H Boucherie. Two-dimensional gel protein database of Saccharomyces cere-visiae (update 1999). Electrophoresis 20 2280-2298, 1999. 

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. 

Regitz-Zagrosek, V., Eleck, E. (1997). Dilated cardiomyopathy-associated proteins and their presentation in a WWW-accessible two-dimensional gel protein database. Electrophoresis 18, 802-808. 

Cells JE, HonoreB, Bauw G, Vandekerckhove J (1990) Comprehensive computerized 2D gel protein databases offer a global approach to the study of the mammalian cell. Bioessays 12 93—97. 

Celis, J. E. (1994) cDNA expression and human 2-D gel protein databases Towards integrating DNA and protein information. Submitted for publication. 

Rasmussen, H. H., Van Damme, J., Puype, M., Gesser, B., Celis, J. E.,and Vandekerckhove, J. (1991) Microsequencing of proteins recorded in human two-dimensional gel protein databases. Electrophoresis 12, 873-882. 

EC02DBASE Escherichia coli gene-protein database (2D gel spots) EC02DBASE)... 

P Touzet, D de Vienne, J-C Huet, C Ouali, F Bouet, M Zivy. Amino acid analysis of proteins separated by two-dimensional gel electrophoresis protein database HEART-2DPAGE a practical approach. Electrophoresis 17 1393-1401,... 

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.

The pursuit of attomole protein identification and peptide sequencing is driven by the need to work at these levels. Although greater confidence will be obtained in MS protein identifications with corrected and enlarged protein databases, identification at reduced amounts is essential. Improvements in mass spectrometers as well as low-level separation techniques are crucial to achieving this goal. Two-dimensional gel analysis of low abundance proteins has limited capabilities, especially for hydrophobic proteins. MS detection limits for peptides have improved by approximately one order of magnitude every 10 years. Detection of zeptomole levels for real samples should soon become a reality. 

FIGURE 4.12 A flow chart showing the basic steps used to identify a protein. The protein is excised from a 2-D electrophoresis gel, the gel diced, and the stain is washed. The protein is reduced and digested in the gel. The newly formed peptides are extracted and analyzed using a MS and/or MS-MS scan mode. The resulting MS and MS-MS data are entered into a protein database search engine that performs the match. 

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