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.
Subject(s)
Databases, Protein , Proteomics , Research Design , Software , Electrophoresis, Gel, Two-DimensionalABSTRACT
Proteios (http://www.proteios.org) is an initiative for the development of a comprehensive open source system for storage, organization, analysis, and annotation of proteomics experiments. The Proteios platform is based on existing principles for proteomics data publishing and data exchange.
Subject(s)
Computational Biology/methods , Proteomics/methods , Software , Mass Spectrometry , User-Computer InterfaceABSTRACT
SUMMARY: PROTEIOS is an initiative for the development of a comprehensive open source system for storage, organization, analysis and annotation of proteomics experiments. The PROTEIOS platform is based on commonly acknowledged principles for proteomics data publishing. AVAILABILITY: http://www.proteios.org
