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2DDB – a bioinformatics solution for analysis of quantitative proteomics data

Malmström, Lars LU ; Marko-Varga, György LU ; Westergren-Thorsson, Gunilla LU ; Laurell, Thomas LU and Malmström, Johan LU (2006) In BMC Bioinformatics 7(158).
Abstract
Background

We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases.



Results

2DDB is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and... (More)
Background

We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases.



Results

2DDB is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and graphical analysis. The current implementation handles quantitative data from 2D gel electrophoresis and multidimensional liquid chromatography/mass spectrometry experiments.



Conclusion

The software has successfully been employed in a number of projects ranging from quantitative liquid-chromatography-mass spectrometry based analysis of transforming growth factor-beta stimulated fi-broblasts to 2D gel electrophoresis/mass spectrometry analysis of biopsies from human cervix. The software is available for download at SourceForge. (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
BMC Bioinformatics
volume
7
issue
158
publisher
BioMed Central
external identifiers
  • WOS:000236762100001
  • PMID:16549013
  • Scopus:33645801199
ISSN
1471-2105
DOI
10.1186/1471-2105-7-158
language
English
LU publication?
yes
id
c48f32ff-0a51-49fe-ad8d-2732ed46ca3e (old id 749035)
alternative location
http://www.biomedcentral.com/1471-2105/7/158
date added to LUP
2007-12-13 15:04:27
date last changed
2016-11-20 04:22:53
@misc{c48f32ff-0a51-49fe-ad8d-2732ed46ca3e,
  abstract     = {Background<br/><br>
We present 2DDB, a bioinformatics solution for storage, integration and analysis of quantitative proteomics data. As the data complexity and the rate with which it is produced increases in the proteomics field, the need for flexible analysis software increases.<br/><br>
<br/><br>
Results<br/><br>
2DDB is based on a core data model describing fundamentals such as experiment description and identified proteins. The extended data models are built on top of the core data model to capture more specific aspects of the data. A number of public databases and bioinformatical tools have been integrated giving the user access to large amounts of relevant data. A statistical and graphical package, R, is used for statistical and graphical analysis. The current implementation handles quantitative data from 2D gel electrophoresis and multidimensional liquid chromatography/mass spectrometry experiments.<br/><br>
<br/><br>
Conclusion<br/><br>
The software has successfully been employed in a number of projects ranging from quantitative liquid-chromatography-mass spectrometry based analysis of transforming growth factor-beta stimulated fi-broblasts to 2D gel electrophoresis/mass spectrometry analysis of biopsies from human cervix. The software is available for download at SourceForge.},
  author       = {Malmström, Lars and Marko-Varga, György and Westergren-Thorsson, Gunilla and Laurell, Thomas and Malmström, Johan},
  issn         = {1471-2105},
  language     = {eng},
  number       = {158},
  publisher    = {ARRAY(0x8e8bd90)},
  series       = {BMC Bioinformatics},
  title        = {2DDB – a bioinformatics solution for analysis of quantitative proteomics data},
  url          = {http://dx.doi.org/10.1186/1471-2105-7-158},
  volume       = {7},
  year         = {2006},
}