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The Proteios Software Environment: an extensible multiuser platform for management and analysis of proteomics data

Häkkinen, Jari LU ; Vincic, Gregory LU ; Månsson, Olle LU ; Wårell, Kristofer LU and Levander, Fredrik LU (2009) In Journal of Proteome Research 8(6). p.3037-3043
Abstract
Proteome analysis involves many steps that generate large quantities of data in different formats. This creates a need for automatic data merging and extraction of important features from data. Furthermore, metadata need to be collected and reported to enable critical evaluation of results. Many data analysis tools are developed locally in research laboratories and are nontrivial to adapt for other laboratories, preventing optimal exploitation of generated data. The proteomics field would benefit from user-friendly analysis and data management platforms in which method developers can make their analysis tools available for the community. Here, we describe the Proteios Software Environment (ProSE) that is built around a Web-based local data... (More)
Proteome analysis involves many steps that generate large quantities of data in different formats. This creates a need for automatic data merging and extraction of important features from data. Furthermore, metadata need to be collected and reported to enable critical evaluation of results. Many data analysis tools are developed locally in research laboratories and are nontrivial to adapt for other laboratories, preventing optimal exploitation of generated data. The proteomics field would benefit from user-friendly analysis and data management platforms in which method developers can make their analysis tools available for the community. Here, we describe the Proteios Software Environment (ProSE) that is built around a Web-based local data repository for proteomics experiments. The application features sample tracking, project sharing between multiple users, and automated data merging and analysis. ProSE has built-in support for several quantitative proteomics workflows, and integrates searching in several search engines, automated combination of the search results with predetermined false discovery rates, annotation of proteins and submission of results to public repositories. ProSE also provides a programming interface to enable local extensions, as well as database access using Web services. ProSE provides an analysis platform for proteomics research and is targeted for multiuser projects with needs to share data, sample tracking, and analysis result. ProSE is open source software available at http://www.proteios.org . (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
in
Journal of Proteome Research
volume
8
issue
6
pages
3037 - 3043
publisher
The American Chemical Society
external identifiers
  • wos:000266719400038
  • scopus:67049100049
ISSN
1535-3893
DOI
10.1021/pr900189c
project
CREATE Health
language
English
LU publication?
yes
id
863d3173-39a6-4555-a867-50a1ef99f067 (old id 1394497)
alternative location
http://pubs.acs.org/doi/abs/10.1021/pr900189c
date added to LUP
2009-05-08 14:05:09
date last changed
2017-11-12 04:08:22
@article{863d3173-39a6-4555-a867-50a1ef99f067,
  abstract     = {Proteome analysis involves many steps that generate large quantities of data in different formats. This creates a need for automatic data merging and extraction of important features from data. Furthermore, metadata need to be collected and reported to enable critical evaluation of results. Many data analysis tools are developed locally in research laboratories and are nontrivial to adapt for other laboratories, preventing optimal exploitation of generated data. The proteomics field would benefit from user-friendly analysis and data management platforms in which method developers can make their analysis tools available for the community. Here, we describe the Proteios Software Environment (ProSE) that is built around a Web-based local data repository for proteomics experiments. The application features sample tracking, project sharing between multiple users, and automated data merging and analysis. ProSE has built-in support for several quantitative proteomics workflows, and integrates searching in several search engines, automated combination of the search results with predetermined false discovery rates, annotation of proteins and submission of results to public repositories. ProSE also provides a programming interface to enable local extensions, as well as database access using Web services. ProSE provides an analysis platform for proteomics research and is targeted for multiuser projects with needs to share data, sample tracking, and analysis result. ProSE is open source software available at http://www.proteios.org .},
  author       = {Häkkinen, Jari and Vincic, Gregory and Månsson, Olle and Wårell, Kristofer and Levander, Fredrik},
  issn         = {1535-3893},
  language     = {eng},
  number       = {6},
  pages        = {3037--3043},
  publisher    = {The American Chemical Society},
  series       = {Journal of Proteome Research},
  title        = {The Proteios Software Environment: an extensible multiuser platform for management and analysis of proteomics data},
  url          = {http://dx.doi.org/10.1021/pr900189c},
  volume       = {8},
  year         = {2009},
}