Bioinformatics as a Tool for Assessing the Quality of Sub-Cellular Proteomic Strategies and Inferring Functions of Proteins: Plant Cell Wall Proteomics as a Test Case

Hélène San Clemente (1) , Rafael F. Pont-Lezica (1) , Elisabeth Jamet (1)

1 SCSV - Surfaces Cellulaires et Signalisation chez les Végétaux

Bioinformatics is used at three different steps of proteomic studies of sub-cellular compartments. First one is protein identifi cation from mass spectrometry data. Second one is prediction of sub-cellular localization, and third one is the search of functional domains to predict the function of identifi ed proteins in order to answer biological questions. The aim of the work was to get a new tool for improving the quality of proteomics of sub-cellular compartments. Starting from the analysis of problems found in databases, we designed a new Arabidopsis database named ProtAnnDB (http://www. polebio.scsv.ups-tlse.fr/ProtAnnDB/). It collects in one page predictions of sub-cellular localization and of functional domains made by available software. Using this database allows not only improvement of interpretation of proteomic data (top-down analysis), but also of procedures to isolate sub-cellular compartments (bottom-up quality control).

Mots clés: bioinformatics; cell wall; plant; proteomics

Domaines: Génomique, Transcriptomique et Protéomique [q-bio.GN]; Bio-informatique [q-bio.QM]

Hélène San Clemente, Rafael F. Pont-Lezica, Elisabeth Jamet. Bioinformatics as a Tool for Assessing the Quality of Sub-Cellular Proteomic Strategies and Inferring Functions of Proteins: Plant Cell Wall Proteomics as a Test Case. Bioinformatics and Biology Insights, 2009, 3, pp.15-28. ⟨hal-00362927⟩