@article{f7d4e68653af4b3384f25f3a2e56c2f2,
title = "A robust and universal metaproteomics workflow for research studies and routine diagnostics within 24 h using phenol extraction, fasp digest, and the metaproteomeanalyzer",
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.",
keywords = "Bioinformatics, Environmental proteomics, Gut microbiome, Mass spectrometry, Microbial communities, Sample preparation, Software",
author = "Robert Heyer and Kay Schallert and Anja B{\"u}del and Roman Zoun and Sebastian Dorl and Alexander Behne and Fabian Kohrs and Sebastian P{\"u}ttker and Corina Siewert and Thilo Muth and Gunter Saake and Udo Reichl and Dirk Benndorf",
note = "Funding Information: RH was supported by a grant of the Federal Ministry of Food, Agriculture and Consumer Protection (BMELV) communicated by the Agency for Renewable Resources (FNR), Grant No.. The authors thank the Information Technology Group of the Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, in particular, Dr. Gerrit Danker. 22404115 (“Biogas Measurement Program III”). KS and RZ were funded by the de.NBI network (“MetaProtServ de-NBI-039”). Funding Information: RH was supported by a grant of the Federal Ministry of Food, Agriculture and Consumer Protection (BMELV) communicated by the Agency for Renewable Resources (FNR), Grant No. Publisher Copyright: {\textcopyright} 2019 Heyer, Schallert, B{\"u}del, Zoun, Dorl, Behne, Kohrs, P{\"u}ttker, Siewert, Muth, Saake, Reichl and Benndorf.",
year = "2019",
doi = "10.3389/fmicb.2019.01883",
language = "English",
volume = "10",
pages = "1883",
journal = "Frontiers in Microbiology",
issn = "1664-302X",
publisher = "Frontiers Media SA",
number = "AUG",
}