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, Dirk Benndorf

Research output: Contribution to journalArticlepeer-review

33 Citations (Scopus)

Abstract

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.

Original languageEnglish
Article number1883
Pages (from-to)1883
JournalFrontiers in Microbiology
Volume10
Issue numberAUG
DOIs
Publication statusPublished - 2019

Keywords

  • Bioinformatics
  • Environmental proteomics
  • Gut microbiome
  • Mass spectrometry
  • Microbial communities
  • Sample preparation
  • Software

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