SWISS-2DPAGE is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database established in 1993. Until March 2011, SWISS-2DPAGE has been maintained, collaboratively, by the Biomedical Proteomics Reasearch Group (BPRG) of the Geneva University and the Proteome Informatics Group of the Swiss Institute of Bioinformatics (SIB). Since April 2011, SWISS-2DPAGE is being maintained by the Swiss-Prot and the Vital-IT of the Swiss Institute of Bioinformatics.
The SWISS-2DPAGE database assembles data on proteins identified on various 2-D and 1-D PAGE maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data (isoelectric point, molecular weight, amino acid composition, peptide masses) and bibliographical references. In addition to this textual data, SWISS-2DPAGE provides several 2-D and 1-D PAGE images showing the experimentally determined location of the protein, as well as a theoretical region, computed from the sequence protein, indicating where the protein might be found in the gel.
Cross-references are provided to Medline and other federated 2-DE databases (Cornea-2DPAGE, COMPLUYEAST-2DPAGE, DOSAC-COBS 2D Page, ECO2DBASE, HSC-2DPAGE, LENS-2DPAGE, OGP-WWW, PHCI-2DPAGE, PMMA-2DPAGE, Siena-2DPAGE, YEPD) and to UniProtKB/Swiss-Prot, which provides many links to other molecular databases (EMBL, Genbank, PROSITE, OMIM, etc).
For detailed information specific to the current SWISS-2DPAGE release, see the release notes.
SWISS-2DPAGE is copyright of the Swiss Institute of Bioinformatics. There are no restrictions on its use by non-profit institutions as long as its content is in no way modified. Any use by and for commercial entities requires a license agreement.
The above copyright notice also applies to any SWISS-2DPAGE documents, including this one.
For details, please refer to the release notes.
You can search SWISS-2DPAGE in differents ways:
You may also:
Hoogland C., Mostaguir K., Sanchez J.-C., Hochstrasser D.F., Appel R.D. SWISS-2DPAGE, ten years later. Proteomics (2004) 4(8): 2352-2356.
Through one of the mirror sites of the ExPASy server, the most efficient and user-friendly way to browse interactively in SWISS-2DPAGE, with active links to other databases:
Downloading SWISS-2DPAGE by FTP:
The directory contains the following files:
The images you can download from the FTP site, in databases/swiss-2dpage/MASTERS directory, are standard TIFF (16Bit) files, thus can be opened with any software supporting this format. The ".mel" extension has been added only to enable viewing the images from a browser when using ImageMaster / Melanie.
The SWISS-2DPAGE user manual (http://world-2dpage.expasy.org/swiss-2dpage/docs/manch2d.html) contains a full description of each type of line, with examples.
You are welcome to use the SWISS-2DPAGE maps, provided you add a copyright notice such as: "Copyright Swiss Institute of Bioinformatics, Geneva, Switzerland".
All the SWISS-2DPAGE protocols (sample preparation, analytical and preparative 2-D PAGE, post-separation analysis) are given at the following location: http://world-2dpage.expasy.org/swiss-2dpage/docs/protocols/
See document at: http://world-2dpage.expasy.org/swiss-2dpage/docs/expl-gifs.html
pI/Mw data given for a SWISS-2DPAGE entry (lines '2D -!- PI/MW') are experimental values, i.e. those read from the reference maps.
pI/Mw data given for a SWISS-2DPAGE entry (lines '2D -!- PI/MW') are experimental values, ie those read from the reference maps. Whereas theoretical pI/Mw are computed from primary amino acids sequence.
The discrepancy between experimental and theoretical values can have several explanations:
The SWISS-2DPAGE flat file (ch2dNN.dat, where NN is the current release number) can be downloaded by FTP (see Availability section of this FAQ).
You are welcome to submit your own gel-based proteomics data to be published in the World-2DPAGE Repository, a public standards-compliant repository for gel-based proteomics data linked to protein identification published in the literature. To do so, use the submision form at: http://world-2dpage.expasy.org/submission/
A software package is available free of charge to build a 2-DE federated database on your own site. This package is called Make2D-DB II, and can be downloaded form HERE.
This tool enables you to easily create a 2-DE database on your Web server, with search functions, such as by accession number, by description, by author, or by clicking on a spot, similar to SWISS-2DPAGE.
The input files to build such a 2-DE database are one or more 2-DE image maps (gif, png, tiff, etc.) with identified protein spots and a text file in which the identified proteins are listed and described (see README file).
Once your database is publicly available, do not hesitate to let us know to include it in the World-2DPAGE Portal