Frontiers in Microbiology (Aug 2019)

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

  • Robert Heyer,
  • Kay Schallert,
  • Anja Büdel,
  • Roman Zoun,
  • Sebastian Dorl,
  • Alexander Behne,
  • Fabian Kohrs,
  • Sebastian Püttker,
  • Corina Siewert,
  • Thilo Muth,
  • Gunter Saake,
  • Udo Reichl,
  • Udo Reichl,
  • Dirk Benndorf,
  • Dirk Benndorf

DOI
https://doi.org/10.3389/fmicb.2019.01883
Journal volume & issue
Vol. 10

Abstract

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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.

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