A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer

The investigation of microbial proteins by mass spectrometry (metaproteomics) is a key technology for simultaneously assessing the taxonomic composition and the functionality of microbial communities in medical, environmental, and biotechnological applications. We present an improved metaproteomics...

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Bibliographic Details
Published in:	Frontiers in microbiology Vol. 10; p. 1883
Main Authors:	Heyer, Robert, Schallert, Kay, Büdel, Anja, Zoun, Roman, Dorl, Sebastian, Behne, Alexander, Kohrs, Fabian, Püttker, Sebastian, Siewert, Corina, Muth, Thilo, Saake, Gunter, Reichl, Udo, Benndorf, Dirk
Format:	Journal Article
Language:	English
Published:	Switzerland Frontiers Media S.A 16-08-2019
Subjects:	bioinformatics environmental proteomics mass spectrometry microbial communities Microbiology sample preparation software environmental proteomics gut microbiome software bioinformatics mass spectrometry microbial communities sample preparation
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Summary:	The investigation of microbial proteins by mass spectrometry (metaproteomics) is a key technology for simultaneously assessing the taxonomic composition and the functionality of microbial communities in medical, environmental, and biotechnological applications. We present an improved metaproteomics workflow using an updated sample preparation and a new version of the MetaProteomeAnalyzer software for data analysis. High resolution by multidimensional separation (GeLC, MudPIT) was sacrificed to aim at fast analysis of a broad range of different samples in less than 24 h. The improved workflow generated at least two times as many protein identifications than our previous workflow, and a drastic increase of taxonomic and functional annotations. Improvements of all aspects of the workflow, particularly the speed, are first steps toward potential routine clinical diagnostics (i.e., fecal samples) and analysis of technical and environmental samples. The MetaProteomeAnalyzer is provided to the scientific community as a central remote server solution at www.mpa.ovgu.de.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 This article was submitted to Systems Microbiology, a section of the journal Frontiers in Microbiology Edited by: Esteban A. Hernandez-Vargas, Frankfurt Institute for Advanced Studies, Germany Equal authorship Reviewed by: Brook Leanne Nunn, University of Washington, United States; Martin Taubert, Friedrich Schiller University Jena, Germany; Carolin Adriane Kolmeder, Max Planck Institute for Developmental Biology, Germany
ISSN:	1664-302X 1664-302X
DOI:	10.3389/fmicb.2019.01883