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JXB Advance Access published online on March 21, 2006
Journal of Experimental Botany, doi:10.1093/jxb/erj139
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© The Author [2006]. Published by Oxford University Press [on behalf of the Society for Experimental Biology]. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org
Received July 8, 2005
Accepted January 26, 2006

Plant Proteomics Special Issue Article

Reproducibility of LC-MS-based protein identification

Matthias Berg 1 *, Axel Parbel 1, Harald Pettersen 2, David Fenyö 2, and Lennart Björkesten 2

1 GE Healthcare, Oskar-Schlemmer-Strasse II, D-80807 München, Germany
2 GE Healthcare, Björkgatan 30, Uppsala, Sweden

* To whom correspondence should be addressed.
Matthias Berg, E-mail: matthias.berg{at}ge.com


  Abstract

Traditional analysis of liquid chromatography-mass spectrometry (LC-MS) data, typically performed by reviewing chromatograms and the corresponding mass spectra, is both time-consuming and difficult. Detailed data analysis is therefore often omitted in proteomics applications. When analysing multiple proteomics samples, it is usually only the final list of identified proteins that is reviewed. This may lead to unnecessarily complex or even contradictory results because the content of the list of identified proteins depends heavily on the conditions for triggering the collection of tandem mass spectra. Small changes in the signal intensity of a peptide in different LC-MS experiments can lead to the collection of a tandem mass spectrum in one experiment but not in another. Also, the quality of the tandem mass spectrometry experiments can vary, leading to successful identification in some cases but not in others. Using a novel image analysis approach, it is possible to achieve repeat analysis with a very high reproducibility by matching peptides across different LC-MS experiments using the retention time and parent mass over charge (m/z). It is also easy to confirm the final result visually. This approach has been investigated by using tryptic digests of integral membrane proteins from organelle-enriched fractions from Arabidopsis thaliana and it has been demonstrated that very highly reproducible, consistent, and reliable LC-MS data interpretation can be made.

Keywords: DeCyderTM MS; differential expression analysis; LC-MS; reproducibility; reversed phase chromatography; nano LC; tandem mass spectrometry.
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