Using the Proteomics Identifications Database (PRIDE)
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
The Proteomics Identifications Database (PRIDE) is a public data repository designed to store, disseminate, and analyze mass spectrometry based proteomics datasets. The PRIDE database can accommodate any level of detailed metadata about the submitted results, which can be queried, explored, viewed, or downloaded via the PRIDE Web interface. The PRIDE database also provides a simple, yet powerful, access control mechanism that fully supports confidential peer?reviewing of data related to a manuscript, ensuring that these results remain invisible to the general public while allowing referees and journal editors anonymized access to the data. This unit describes in detail the functionality that PRIDE provides with regards to searching, viewing, and comparing the available data, as well as different options for submitting data to PRIDE. Curr. Protoc. Bioinform. 21:13.8.1?13.8.19. © 2008 by John Wiley & Sons, Inc.
Keywords: PRIDE; proteomics; identifications; database; repository; standards
Table of Contents
- Introduction
- Basic Protocol 1: Data Retrieval Using the PRIDE Web Interface
- Basic Protocol 2: Data Retrieval Using the PRIDE BioMart
- Basic Protocol 3: Data Submission to PRIDE
- Support Protocol 1: Preparing a PRIDE Submission Using the Proteome Harvest Excel Workbook
- Support Protocol 2: Preparing a PRIDE Submission Using the PRIDE API
- Guidelines for Understanding Results
- Commentary
- Literature Cited
- Figures
- Tables
Materials
Figures
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Figure 13.8.1 The PRIDE homepage. View Image -
Figure 13.8.2 This form is used to view, download, or compare PRIDE experiments. View Image -
Figure 13.8.3 The PRIDE Advanced Search page. One of the following types of query can be performed at one time using this page: by PRIDE experiment accession, by identified protein accession, by peptide sequence, or by controlled vocabulary annotations on the experimental sample. View Image -
Figure 13.8.4 The PRIDE Browse Experiments page. This page provides an entry point to obtain data from PRIDE based on spectrum availability, project description, source organism taxonomy, source tissue annotations (tissue, cell type, function, and/or localization), and disease phenotype. Clicking on any link will perform a search on the selected parameter and take you to the Search Results summary page. View Image -
Figure 13.8.5 The PRIDE BioMart homepage. View Image -
Figure 13.8.6 The first page of the PRIDE data submission form. Note that the option to keep data private is selected by default. View Image -
Figure 13.8.7 The Microsoft Excel Security Warning dialogue will be displayed the first time the Proteome Harvest PRIDE submission spreadsheet is opened. View Image -
Figure 13.8.8 The Parameter Entry Form provides direct access to the Ontology Lookup Service at the EBI that can be used to select appropriate terms from over 50 different ontologies and controlled vocabularies. View Image
Videos
Literature Cited
| Literature Cited | |
| Côté, R.G., Jones, P., Apweiler, R., and Hermjakob, H. 2006. The Ontology Lookup Service, a lightweight cross‐platform tool for controlled vocabulary queries. BMC Bioinformatics 7: 97. | |
| Jones, P., Côté, R.G., Martens, L., Quinn, A.F., Taylor, C.F., Derache, W., Hermjakob, H., and Apweiler, R. 2006. PRIDE: A public repository of protein and peptide identifications for the proteomics community. Nucleic Acids Res. 34: D659‐D663. | |
| Martens, L., Hermjakob, H., Jones, P., Adamski, M., Taylor, C., States, D., Gevaert, K., Vandekerckhove, J., and Apweiler, R. 2005. PRIDE: The proteomics identifications database. Proteomics 5: 3537‐3545. |
