F. Levander, M. Krogh, K. Wårell, P. Gärdén, P. James and J. Häkkinen
Automated reporting from gel-based proteomics experiments using the open
source Proteios database application
Proteomics 7, 668-674 (2007)
Abstract: The assembly of data from
different parts of proteomics workflows 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 pre-determined error rate are also
explicitly calculated for proteins that appear on the result lists of
more than one search engine
LU TP 06-42