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Automated reporting from gel‐based proteomics experiments using the open source Proteios database application
Author(s) -
Levander Fredrik,
Krogh Morten,
Wårell Kristofer,
Gärdén Per,
James Peter,
Häkkinen Jari
Publication year - 2007
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.200600814
Subject(s) - workflow , proteomics , bottleneck , identification (biology) , computer science , database search engine , open source , software , shotgun proteomics , data mining , database , information retrieval , search engine , biology , biochemistry , botany , programming language , gene , embedded system
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.