World-2DPAGE Home

Frequently Asked Questions
about SWISS-2DPAGE


  1. What is SWISS-2DPAGE ?
  2. Copyright notice
  3. Current content of the SWISS-2DPAGE database
  4. How to search in SWISS-2DPAGE ?
  5. How to cite SWISS-2DPAGE ?
  6. Availability of SWISS-2DPAGE
  7. Where do I download the SWISS-2DPAGE images ?
  8. What is the meaning/content of the different lines of a SWISS-2DPAGE entry ?
  9. Can I use the SWISS-2DPAGE images for educational or training purposes ?
  10. I would like information about protocols used for the SWISS-2DPAGE sample preparation
  11. How to interpret a protein map ?
  12. What is the source of pI/Mw values given in SWISS-2DPAGE entries ?
  13. Why are pI/Mw values given in SWISS-2DPAGE entries in some cases far from theoretical values ?
  14. How to index SWISS-2DPAGE with SRS ?
  15. Collecting 2-DE maps from other groups
  16. How to create a 2-DE database ?

  1. What is SWISS-2DPAGE ?
  2. 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.

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  3. Copyright notice
  4. 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.

    For information about the licensing scheme see: license or contact us.

    The above copyright notice also applies to any SWISS-2DPAGE documents, including this one.

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  5. Current content of the SWISS-2DPAGE database
  6. For details, please refer to the release notes.

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  7. How to search in SWISS-2DPAGE ?
  8. You can search SWISS-2DPAGE in differents ways:

    You may also:

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  9. How to cite SWISS-2DPAGE ?
  10. Hoogland C., Mostaguir K., Sanchez J.-C., Hochstrasser D.F., Appel R.D. SWISS-2DPAGE, ten years later. Proteomics (2004) 4(8): 2352-2356.

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  11. Availability of SWISS-2DPAGE
  12. 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:

    • ch2dNN.dat: the SWISS-2DPAGE data text file (the whole identified proteins), for the current release
    • shortdes.txt: Short description of entries in SWISS-2DPAGE
    • manch2d.html: User manual
    • relnotes.html: Release notes
    • license.txt: Important information concerning SWISS-2DPAGE
    • the subdirectory "MASTERS", containing itself the reference map images in the ImageMaster / Melanie format (TIFF, 16Bit).
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  13. Where do I download the SWISS-2DPAGE images ?
  14. 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.

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  15. What is the meaning/content of the different lines of a SWISS-2DPAGE entry ?
  16. 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.

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  17. Can I use the SWISS-2DPAGE images for educational or training purposes ?
  18. You are welcome to use the SWISS-2DPAGE maps, provided you add a copyright notice such as: "Copyright Swiss Institute of Bioinformatics, Geneva, Switzerland".

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  19. I would like information about protocols used for the SWISS-2DPAGE Sample preparation
  20. 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/

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  21. How to interpret a protein map ?
  22. See document at: http://world-2dpage.expasy.org/swiss-2dpage/docs/expl-gifs.html

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  23. What is the source of pI/Mw values given in SWISS-2DPAGE entries ?
  24. pI/Mw data given for a SWISS-2DPAGE entry (lines '2D -!- PI/MW') are experimental values, i.e. those read from the reference maps.

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  25. Why are pI/Mw values given in SWISS-2DPAGE entries in some cases far from theoretical values ?
  26. 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:

    • Post-translational modifications can considerably influence pI/Mw of a mature protein. But until now, no tool exists to predict this influence, especially on the pI level. Thus theoretical values are calculated from the raw amino acid sequence, without taking into account post-translational modifications.
    • Proteins seen on 2-DE gel may have been degraded either during the sample preparation or during the migration, thus leading to fragments. We have some evidence for this kind of data (see for example, protein RuBisCo: http://world-2dpage.expasy.org/swiss-2dpage/O03042).
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  27. How to get SWISS-2DPAGE in data text format ?
  28. 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).

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  29. Collecting 2-DE maps from other groups
  30. 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/

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  31. How to create a 2-DE database
  32. 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

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