From Human Salivary Proteome Wiki
Proteomics Database
In addition to the wiki engine, a dedicated database has been incorporated to the Human Salivary Proteome Wiki to store all the MS/MS data submitted by the community. This database is known as the PRoteomics IDEntifications database or PRIDE. It is a standards-compliant database with support for various proprietary data formats as well. The database consists or mass spectra, peptide and protein identifications, and protocol metadata. To maximize search performance, a data warehouse optimized for large-scale querying is used to mirror the data stored in PRIDE. For more information about PRIDE and the BioMart data warehouse, please see https://www.ebi.ac.uk/pride/markdownpage/documentationpage.
The wiki has several interfaces to seamlessly interacts with our local instance of PRIDE and BioMart. It provides a single point of submission and can exchange data with other proteomics repositories. In addition, the wiki also leverages the data stored in the proteomics database to automatically determine which proteins can be classified as salivary proteins and measures their abundance through sequence coverage and the number of peptide hits.
See also: Help:Salivary Proteins
Contents |
Browsing and Searching
To view the proteomics data associated with a particular protein, click on the Tools tab on the protein page, and select Proteomics Identifications. The list of experiments that have identified the protein will be shown. A search interface is also available for you to query for experiments and identifications using one of the five attributes listed. For example, you can look for proteins using any accession numbers of your choice (e.g. UniProt or IPI) with the "Any mapped protein accession" field. For more information about this search tool, see Help:Searching#Experiment_Search.
Experiment List
The data stored in the database is organized hierarchically in the order of experiments, protein identifications, and peptide identifications. As a result, the initial returns from your search or through the protein pages are experiments that contain items of your interest. Figure 1 shows the result table which also indicates the number of proteins and peptides that match the query. If your search is not protein or peptide specific, then the counts will show all the identifications from the corresponding experiment. More information about the experiments can be retrieved by clicking the links in the Accession column of the table.
Experiment Details
Figure 2 shows a table containing detailed information about an experiment. It lists contact information of the person who submitted the data, properties of the tissue sample, citations, and other metadata describing the protocol. The "View identification details" link will take you to a list that shows all the proteins identified in this experiment.
Identifications
Protein and peptide identifications are generated by matching MS/MS spectra to a protein database (see Figure 3). Traditionally, the International Protein Index (IPI) is the database of choice. However, UniProt has become more and more popular as the number of sequences it indexes continues to improve. The protein and peptide identifications tables list the output from the spectra search. Note that the same attribute may have different meaning or can be calculated differently depending on the search engine used (e.g. SEQUEST, Mascot, X! Tandem, etc.). Please refer to the the appropriate documentations when interpreting these data.
References
Vizcaíno JA, et al. (2009) A guide to the Proteomics Identifications Database proteomics data repository. Proteomics 9(18):4276-83 [PubMed:19662629]
Haider S, et al. (2009) BioMart Central Portal--unified access to biological data. Nucleic Acids Res. 37(Web Server issue):W23-7 [PubMed:19420058]
