An iterative workflow for mining the human intestinal metaproteome

BMC Genomics

Research Article

Mark de Been¹  Carolin Kolmeder¹  Willem M de Vos²  Christian Beauvallet³  Joël Doré⁴  Catherine Juste⁴  Sjef Boeren⁵  Koos Rooijers⁶  Peter J Schaap⁶  Pilar Galan⁷ 

[1] Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, FIN-00014, Helsinki, Finland;Department of Veterinary Biosciences, Division of Microbiology and Epidemiology, University of Helsinki, P.O. Box 66, FIN-00014, Helsinki, Finland;Laboratory of Microbiology, Wageningen University, Dreijenplein 10, 6703, Wageningenthe Netherlands, HB;INRA, IsoCellExpress (ICE), UMR 1313 GABI, 78350, Jouy-en-Josas, France;INRA, UMR 1319, 78350, Micalis, Jouy-en-Josas, France;Laboratory of Biochemistry, Wageningen University, Dreijenlaan 10, 6703, Wageningen, HB, The Netherlands;Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein10, 6703, Wageningen, HB, The Netherlands;UMR U557 INSERM, U1125 INRA, CNAM, Université Paris 13, F-93017, Bobigny, France;

关键词: Metagenomic Data;    Human Microbiome Project;    Average Nucleotide Identity;    Lactobacillus Reuteri;    False Discovery Rate Estimation;   

DOI  :  10.1186/1471-2164-12-6

 received in 2010-09-03, accepted in 2011-01-05,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundPeptide spectrum matching (PSM) is the standard method in shotgun proteomics data analysis. It relies on the availability of an accurate and complete sample proteome that is used to make interpretation of the spectra feasible. Although this procedure has proven to be effective in many proteomics studies, the approach has limitations when applied on complex samples of microbial communities, such as those found in the human intestinal tract. Metagenome studies have indicated that the human intestinal microbiome contains over 100 times more genes than the human genome and it has been estimated that this ecosystem contains over 5000 bacterial species. The genomes of the vast majority of these species have not yet been sequenced and hence their proteomes remain unknown. To enable data analysis of shotgun proteomics data using PSM, and circumvent the lack of a defined matched metaproteome, an iterative workflow was developed that is based on a synthetic metaproteome and the developing metagenomic databases that are both representative for but not necessarily originating from the sample of interest.ResultsTwo human fecal samples for which metagenomic data had been collected, were analyzed for their metaproteome using liquid chromatography-mass spectrometry and used to benchmark the developed iterative workflow to other methods. The results show that the developed method is able to detect over 3,000 peptides per fecal sample from the spectral data by circumventing the lack of a defined proteome without naive translation of matched metagenomes and cross-species peptide identification.ConclusionsThe developed iterative workflow achieved an approximate two-fold increase in the amount of identified spectra at a false discovery rate of 1% and can be applied in metaproteomic studies of the human intestinal tract or other complex ecosystems.

【 授权许可】

Unknown   
© Rooijers et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.