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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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2019
Materias:
Microbiology
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707425/
https://www.ncbi.nlm.nih.gov/pubmed/31474963
http://dx.doi.org/10.3389/fmicb.2019.01883
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author 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
author_facet 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
author_sort Heyer, Robert
collection PubMed
description 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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spelling pubmed-67074252019-08-30 A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer 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 Front Microbiol Microbiology 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. Frontiers Media S.A. 2019-08-16 /pmc/articles/PMC6707425/ /pubmed/31474963 http://dx.doi.org/10.3389/fmicb.2019.01883 Text en Copyright © 2019 Heyer, Schallert, Büdel, Zoun, Dorl, Behne, Kohrs, Püttker, Siewert, Muth, Saake, Reichl and Benndorf. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
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
A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer
title A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer
title_full A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer
title_fullStr A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer
title_full_unstemmed A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer
title_short A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer
title_sort robust and universal metaproteomics workflow for research studies and routine diagnostics within 24 h using phenol extraction, fasp digest, and the metaproteomeanalyzer
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707425/
https://www.ncbi.nlm.nih.gov/pubmed/31474963
http://dx.doi.org/10.3389/fmicb.2019.01883
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