SWISS-PROT peptide database

Increasing reproducibility of available separation techniques and sensitivity and affordability of mass spectrometers, as well as the desire and need to automate the identification process, have caused peptide mass fingerprinting and MS/MS sequencing to gain importance and to become the method of choice for many proteomics laboratories. Several tools are available to assist users in the interpretation of mass spectrometry data. Peptldent (http //www.expasy.org/tools/peptident.html) on the ExPASy server follows the concept of the other tools from the ExPASy proteomics suite, in that it takes into account annotation available in the SWISS-PROT/TrEMBL database, in particular as post-translational modifications and processing are concerned. The user can paste peptide masses (monoisotopic or average) into the Peptldent form, but peptide mass data can also be uploaded from a file on the user s local computer. Supported file formats are .pkm ... 

To estimate the number of genes expressing products that could be accessible to antibody therapeutics, we assume that proteins are required to be located in the extracellular matrix. We also assume that the extracellular location is the union of secreted and transmembrane sets of proteins. Where the extracellular location is known, this is often included in Swiss-Prot and gene ontology (GO) [37] database annotation for the protein. Secreted proteins can be predicted by the presence of a signal peptide whilst transmembrane... 

Table 12 Identification of G3PC ARATH (GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE, CYTOSOUC), Species Arabidopsis thaliana, SWISS-PROT (SP) entry P25858 using different PMF tools. The restricting parameters used were Arabidopsis thaliana for the species, a minimum number of 4 matched masses, a maximal tolerance for masses of 60 ppm, at most one missed cleavage of tryptic peptides allowed, and the modifications accepted were oxidised methionines and cysteines treated with iodoacetamide to form carboxyamidomethyl cysteines. The databases queried by each program are listed in the right column. In the score column, the first value is the score of the first candidate protein, followed by either the score of the second candidate protein (if the first one is the correct one)...

Table 13 Query for 60 mass values of a MALDI-TOF MS spectrum from a mixture of P0N2JHIUMAN (SERUM PARAOXONASE/ARYLESTERASE 2, Species Homo sapiens, SWISS-PROT accession number Q15165) and the marker GT26J5CHJA (GLUTATHIONE S-TRANSFERASE 26 KDA, Species Schistosoma japonicum, SWISS-PROT accession number P08515). The query was made for the all available species, the minimum number of matched masses was 4, the maximal tolerance for masses was 40 ppm, at most one missed cleavage for tryptic peptides was allowed, and the modifications accepted were artefactual modification of cysteines with acrylamide and oxidised methionines. Mr values were delimited between 20 and 40 kDa. The databases queried by each program are listed in the right column...

The purpose of the molecular scanner is for the identification of proteins that were separated with a 2-DE gel. Therefore, for each scan point, the lists of peptide masses are submitted to the peptide mass fingerprint identification program Smartldent [51], which searches the protein sequence database SWISS-PROT and returns a list of matching proteins and their score. 

Comparison of identification scores as found from MASCOT interrogation using Swiss-Prot database and R. norvegicustamwmy for four peptides before and after automated derivatization with 3-SBASE... 

Very few protein sequences in Insecta are entered into the SWISS-PROT database, and even fewer protein sequences from genus Spodoptera are found in the database (78 in Uni-ProtKB/SWISS-PROT Release 55.6, 01-July-2008). Moreover, very few GST proteins from the Lepidoptera family are available. Because none of the tryptic peptides from Spodoptera frugiperda GST matched identically to the template Manduca sexta GST), mass-spectrometry-based methods for de novo sequencing is a powerful approach for identification of unknown proteins that may be homologous to proteins from other species. 

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