Protein identification resource database

The first resources for computer modeling of protein structure are the nucleic acid and protein sequence databases (see Table 6.1), curated by the European Molecular Biology Laboratory (EMBL) in Europe, the National Center for Biotechnology Information (GenBank at the NCBl) in the United States, and the DNA Database of Japan (DDBJ) in Japan. These databases are accessible via the Internet, and most likely one s own scientific institution maintains a local version, which is updated through CD-ROMs released quarterly. Perhaps the predominant protein sequence database is SWISS-PROT. - Others include the nonredundant protein sequence database (OWL) and the protein identification resource database (PIR). ... 

An important development in high-throughput protein identifieation is the introduction of protein database searching [111]. After separation on ID- or 2D-GE, the proteins were blotted onto a membrane and enzymatically digested after reduction and alkylation. The tryptic peptide mixture is analysed by MALDl-MS to achieve a peptide map or peptide mass fingerprint (PMF). The m/z information of the peptides is used to search the protein database, e.g., the Protein Identification Resource (PIR) database [112-114]. If the mass of just 4-6 tryptic peptides is accurately measured (between 0.1 and 0.01%), a useful database search can be performed. 

Proteomics is concerned with the analysis of the complete protein complements of genomes. Thus proteomics includes not only the identification and quantification of proteins, but also the determination of their localization, modifications, interactions, activities, and functions. This chapter focuses on protein sequences as the sources of biochemical information. Protein sequence databases are surveyed. Similarity search and sequence alignments using the Internet resources are described. 

A comprehensive description of the databases and methods for domain, family, and pattern identification is available in chapter 2. Therefore, in this chapter, the discussion of the application of family and domain information to function assignment will be limited to Pfam, the virtual standard in protein domain/family classification, and to InterPro and CDD, two resources that integrate multiple domain databases. In addition, I discuss tools that can be used to scan those databases, namely HMMER,... 

The Universal Protein Resource (UniProt) provides the scientific community with a centralized, authoritative resource for protein sequences and functional information with three database components. (1) The UniProt Knowledgebase (UniProtKB), produced by a combination of automation and over 25 years of human curation, is the central protein sequence database with accurate, consistent, functional annotation and extensive cross-references. (2) The UniProt Reference Clusters (UniRef) provide clustered sets of sequences from UniProtKB (including splice variants and isoforms) in order to obtain complete coverage of sequence space at several resolutions. The UniRef 100 database is particularly useful for Mass Spec identifications as it exposes known sequence variation and splice-form annotation contained in UniProtKB records. (3) The UniProt Archive (UniParc) provides a stable comprehensive sequence collection by storing the complete body of all publicly available protein sequence data. 

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