TY - JOUR T1 - A Robust and Universal Metaproteomics Workflow for Research Studies and Routine Diagnostics Within 24 h Using Phenol Extraction, FASP Digest, and the MetaProteomeAnalyzer AU - Heyer, Robert AU - Schallert, Kay AU - Büdel, Anja AU - Zoun, Roman AU - Dorl, Sebastian AU - Behne, Alexander AU - Kohrs, Fabian AU - Püttker, Sebastian AU - Siewert, Corina AU - Muth, Thilo AU - Saake, Gunter AU - Reichl, Udo AU - Benndorf, Dirk AB - 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. KW - bioinformatics KW - software KW - sample preparation KW - environmental proteomics KW - microbial communities KW - mass spectrometry KW - gut microbiome KW - 610 Medizin und Gesundheit PY - 2019 LA - eng PB - Robert Koch-Institut JO - Frontiers in Microbiology VL - 10 IS - 1883 SP - 1 EP - 20 DO - 10.3389/fmicb.2019.01883 ER -