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2017-06-15 - Colloque/Présentation - communication orale - Anglais - 19 page(s)

Beraud Mélanie , Giambarresi Giuseppe , Gillan David , Wattiez Ruddy , "Evaluation of the SWATH-MS potential for comparative metaproteomic of complex ecosystems" in 2nd International Metaproteomics Symposium, Alghero, Italie, 2017

  • Codes CREF : Biochimie (DI3112), Biologie moléculaire (DI3111), Biologie (DI3100), Microbiologie et protistologie [bacteriol.,virolog.,mycolog.] (DI3130), Ecologie (DI3123)
  • Unités de recherche UMONS : Protéomie et Microbiologie (S828)
  • Instituts UMONS : Institut des Biosciences (Biosciences)
Texte intégral :

Abstract(s) :

(Anglais) Background Since 2012, the SWATH-MS approach has proved to be very useful on various samples by increasing the accuracy of protein quantification. To the best of our knowledge, the method was never applied to the study of synthetic microbial ecosystems. Methods The SWATH-MS approach was applied to study a synthetic microbial community. Nine bacterial species were cultivated as a mixed community in a marine medium at 16°C. After 28 days of growth, the structure of the community was evaluated by quantitative PCR and was shown to be highly uneven. Proteins were extracted and LC-MS/MS were conducted in SWATH mode. In parallel, single-species cultures in the same conditions were performed. Proteins were extracted and a data-dependent (DDA)-MS analyses was conducted. From these results, a series of spectral libraries of different species composition was computed and matched with the SWATH-MS data of the community. The number of proteins identified as well as accuracy of quantification were recovered for each match. Results Using the SWATH-MS approach, we increased the number of identified proteins by 2- fold for the rare species, contrary to the classical DDA approach where rare species were almost invisible. Furthermore, the accuracy of the quantification was largely improved. The potential to evaluate taxon abundance and the number of species that should be used to build the spectral library will be discussed. Conclusions SWATH-MS is a very promising tool in the field of experimental environmental microbiology. PROS and CONS will be presented.