About Proteios Software Environment

Proteios SE is a multi-user platform for analysis and management of proteomics data.

Proteios SE (or ProSE) is meant to be installed on a local server in a proteomics laboratory. The server is accessed using any web browser using personal login accounts with administrated access levels. With his or her own account, a user can enter data into the database, group experiments together into projects, run protein identification engines and other analysis tools. Users can choose to share almost any database item (e.g. samples, data, experiments, files, etc) with other users to facilitate online collaboration.

Notes on Proteios 1.x

Proteios SE (Proteios 2.x) is a major rewrite of version 1.x and will not support data migration from 1.x

Origin of Name

Designed for proteomics, the study of proteins, Proteios takes its name from the Greek word πρώτειος for "primary, first and foremost", the word that inspired the name "proteins" for this important class of molecules.

How to Cite

Proteios Software Environment is described in this article:

  • Häkkinen J, Vincic G, Månsson O, Wårell K and Levander F. The Proteios Software Environment - An extensible multi-user platform for management and analysis of proteomics data. J Proteome Res 2009 DOI: 10.1021/pr900189c.

If you use Proteios SE in your work, please cite the above article and the URL.

The alignment algorithm for the label free quantification workflow in Proteios is described here:

  • Sandin M, Ali A, Hansson K, Månsson O, Andreasson E, Resjö S, Levander F. An adaptive alignment algorithm for quality-controlled label-free LC-MS. Mol Cell Proteomics 2013 DOI:10.1074/mcp.O112.021907.

Some of the methods and concepts in Proteios SE have been transferred from Proteios 1.x, and have been published previously:

  • Levander F, Krogh M, Wårell K, Gärdén P, James P, Häkkinen J. Automated reporting from gel-based proteomics experiments using the open source Proteios database application. Proteomics. 2007 Mar;7(5):668-74. abstract
  • Gärdén P, Alm R, Häkkinen J. PROTEIOS: an open source proteomics initiative. Bioinformatics. 2005 May 1;21(9):2085-7. Epub 2005 Feb 3. full text


Development of Proteios SE has been generously supported by:

Lund University through SCIBLU

Swedish Foundation for Strategic Research through CREATE Health and the Late Blight Disease in Potato program.

The Swedish Research Council through BILS and grant 2007-5188.

ProDaC - The Proteomics Data Collection FP6 European Union program

Last modified 12 months ago Last modified on Jun 9, 2021, 7:42:15 PM