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Automated reporting from gel-based proteomics experiments using the open source Proteios database application

Levander, Fredrik LU ; Krogh, Morten LU ; Wårell, Kristofer LU ; Gärdén, Per LU ; James, Peter LU and Häkkinen, Jari LU (2007) In Proteomics 7(5). p.668-674
Abstract
The assembly of data from different parts of proteomics workflow is often a major bottleneck in proteomics. Furthermore, there is an increasing demand for the publication of details about protein identifications due to the problems with false-positive and false-negative identifications. In this report, we describe how the open-source Proteios software has been expanded to automate the assembly of the different parts of a gel-based proteomics workflow. In Proteios it is possible to generate protein identification reports that contain all the information currently required by proteomics journals. It is also possible for the user to specify maximum allowed false positive ratios, and reports are automatically generated with the corresponding... (More)
The assembly of data from different parts of proteomics workflow is often a major bottleneck in proteomics. Furthermore, there is an increasing demand for the publication of details about protein identifications due to the problems with false-positive and false-negative identifications. In this report, we describe how the open-source Proteios software has been expanded to automate the assembly of the different parts of a gel-based proteomics workflow. In Proteios it is possible to generate protein identification reports that contain all the information currently required by proteomics journals. It is also possible for the user to specify maximum allowed false positive ratios, and reports are automatically generated with the corresponding score cut-offs calculated. When protein identification is conducted using multiple search engines, the score thresholds that correlate to the predetermined error rate are also explicitly calculated for proteins that appear on the result lists of more than one search engine. (Less)
Please use this url to cite or link to this publication:
author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
2-D PAGE, protein identification, reporting
in
Proteomics
volume
7
issue
5
pages
668 - 674
publisher
John Wiley & Sons
external identifiers
  • wos:000245158500003
  • scopus:33947434519
ISSN
1615-9861
DOI
10.1002/pmic.200600814
language
English
LU publication?
yes
id
da5ec110-45d6-4650-857d-ceec2fb070f0 (old id 669565)
date added to LUP
2007-12-14 14:20:22
date last changed
2017-01-01 05:12:20
@article{da5ec110-45d6-4650-857d-ceec2fb070f0,
  abstract     = {The assembly of data from different parts of proteomics workflow is often a major bottleneck in proteomics. Furthermore, there is an increasing demand for the publication of details about protein identifications due to the problems with false-positive and false-negative identifications. In this report, we describe how the open-source Proteios software has been expanded to automate the assembly of the different parts of a gel-based proteomics workflow. In Proteios it is possible to generate protein identification reports that contain all the information currently required by proteomics journals. It is also possible for the user to specify maximum allowed false positive ratios, and reports are automatically generated with the corresponding score cut-offs calculated. When protein identification is conducted using multiple search engines, the score thresholds that correlate to the predetermined error rate are also explicitly calculated for proteins that appear on the result lists of more than one search engine.},
  author       = {Levander, Fredrik and Krogh, Morten and Wårell, Kristofer and Gärdén, Per and James, Peter and Häkkinen, Jari},
  issn         = {1615-9861},
  keyword      = {2-D PAGE,protein identification,reporting},
  language     = {eng},
  number       = {5},
  pages        = {668--674},
  publisher    = {John Wiley & Sons},
  series       = {Proteomics},
  title        = {Automated reporting from gel-based proteomics experiments using the open source Proteios database application},
  url          = {http://dx.doi.org/10.1002/pmic.200600814},
  volume       = {7},
  year         = {2007},
}