DbSAP:Single Amino Acid Polymorphisms Database

Because of its high throughput and gradually improvement in the resolution, shotgun proteomics becomes one of the most popular methods for proteome characterization. Tandem mass spectra peptides gotten from LC MS/MS experiments then need to be compared to the theoretical spectra derived from a reference protein database, i.e. the database search engine method. However, with the improvement of the resolution of mass spectrometer, the identification power of mass spectrometry data did not increase at the same time. At present, the detection rate of mass spectra data is usually about 20%, which is not consistent with our purposes of studying proteome and the biological process they participate in. The reason may be the protein sequence databases we usually used do not contain information about protein variants. When we use wild-type database search engine to identify protein, variant peptides and proteins will not been identified. While mutant proteins encoded by a single nucleotide polymorphism or gene mutation are existent, especially the mutant secreted protein which may be associated with the occurrence of disease. Essentially, the mutant protein is the amino acid mutation, so the single amino acid polymorphism database for our study of the protein variation is crucial.Here, we collected the SNP and mutant information from eight related database: dbSNP, Cosmic, HPMD, Ensembl, Uniprot, PMD, MSIPI, CanProVar. Then we build a comprehensive variation-containing protein database. According to the protein variations database, we get 907211 atlases and 4358 high quality peptides by database search engine. Taking advantage of the peptides, proteins and gene information, and combining the diseases and drug targets information, we provide a convenient and intuitive information resource database for the related researchers.