TY - JOUR A1 - Van Den Bossche, T. A1 - Arntzen, M. O. A1 - Becher, D. A1 - Benndorf, D. A1 - Eijsink, V. G. H. A1 - Henry, C. A1 - Jagtap, P. D. A1 - Jehmlich, N. A1 - Juste, C. A1 - Kunath, B. J. A1 - Mesuere, B. A1 - Muth, Thilo A1 - Pope, P. B. A1 - Seifert, J. A1 - Tanca, A. A1 - Uzzau, S. A1 - Wilmes, P. A1 - Hettich, R. L. A1 - Armengaud, J. T1 - The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes N2 - Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time. The international metaproteomics community is delighted to announce the launch of the Metaproteomics Initiative (www.metaproteomics.org), the goal of which is to promote dissemination of metaproteomics fundamentals, advancements, and applications through collaborative networking in microbiome research. The Initiative aims to be the central information hub and open meeting place where newcomers and experts interact to communicate, standardize, and accelerate experimental and bioinformatic methodologies in this feld. We invite the entire microbiome community to join and discuss potential synergies at the interfaces with other disciplines, and to collectively promote innovative approaches to gain deeper insights into microbiome functions and dynamics. KW - Microbiome KW - Metaproteomics KW - Networking KW - Meta-Omics KW - Interactions KW - Education PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-542290 DO - https://doi.org/10.1186/s40168-021-01176-w VL - 9 IS - 1 SP - 243 PB - BMC AN - OPUS4-54229 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Van Den Bossche, T. A1 - Kunath, B. A1 - Schallert, K. A1 - Schäpe, S. A1 - Abraham, P. E. A1 - Armengaud, J. A1 - Arntzen, M. Ø. A1 - Bassignani, A. A1 - Benndorf, D. A1 - Fuchs, S. A1 - Giannone, R. J. A1 - Griffin, T. J. A1 - Hagen, L. H. A1 - Halder, R. A1 - Henry, C. A1 - Hettich, R. L. A1 - Heyer, R. A1 - Jagtap, P. A1 - Jehmlich, N. A1 - Jensen, M. A1 - Juste, C. A1 - Kleiner, M. A1 - Langella, O. A1 - Lehmann, T. A1 - Leith, E. A1 - May, P. A1 - Mesuere, B. A1 - Miotello, G. A1 - Peters, S. L. A1 - Pible, O. A1 - Queiros, P. T. A1 - Reichl, U. A1 - Renard, B. Y. A1 - Schiebenhoefer, H. A1 - Sczyrba, A. A1 - Tanca, A. A1 - Trappe, K. A1 - Trezzi, J.-P. A1 - Uzzau, S. A1 - Verschaffelt, P. A1 - von Bergen, M. A1 - Wilmes, P. A1 - Wolf, M. A1 - Martens, L. A1 - Muth, Thilo T1 - Critical Assessment of MetaProteome Investigation (CAMPI): A multi-laboratory comparison of established workflows N2 - Metaproteomics has matured into a powerful tool to assess functional interactions in microbial communities. While many metaproteomic workflows are available, the impact of method choice on results remains unclear. Here, we carry out a community-driven, multi-laboratory comparison in metaproteomics: the critical assessment of metaproteome investigation study (CAMPI). Based on well-established workflows, we evaluate the effect of sample preparation, mass spectrometry, and bioinformatic analysis using two samples: a simplified, laboratory-assembled human intestinal model and a human fecal sample. We observe that variability at the peptide level is predominantly due to sample processing workflows, with a smaller contribution of bioinformatic pipelines. These peptide-level differences largely disappear at the protein group level. While differences are observed for predicted community composition, similar functional profiles are obtained across workflows. CAMPI demonstrates the robustness of present-day metaproteomics research, serves as a template for multi-laboratory studies in metaproteomics, and provides publicly available data sets for benchmarking future developments. KW - Metaproteomics KW - Mass spectrometry KW - Data science KW - Benchmarking KW - Bioinformatics PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-541220 DO - https://doi.org/10.1038/s41467-021-27542-8 SN - 2041-1723 VL - 12 SP - 1 EP - 15 PB - Nature Publishing Group CY - London AN - OPUS4-54122 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Pech, S. A1 - Rehberg, M. A1 - Janke, R. A1 - Benndorf, D. A1 - Genzel, Y. A1 - Muth, Thilo A1 - Sickmann, A. A1 - Rapp, E. A1 - Reichl, U. T1 - Tracking changes in adaptation to suspension growth for MDCK cells: cell growth correlates with levels of metabolites, enzymes and proteins N2 - Adaptations of animal cells to growth in suspension culture concern in particular viral vaccine production, where very specific aspects of virus-host cell interaction need to be taken into account to achieve high cell specific yields and overall process productivity. So far, the complexity of alterations on the metabolism, enzyme, and proteome level required for adaptation is only poorly understood. In this study, for the first time, we combined several complex analytical approaches with the aim to track cellular changes on different levels and to unravel interconnections and correlations. Therefore, a Madin-Darby canine kidney (MDCK) suspension cell line, adapted earlier to growth in suspension, was cultivated in a 1-L bioreactor. Cell concentrations and cell volumes, extracellular metabolite concentrations, and intracellular enzyme activities were determined. The experimental data set was used as the input for a segregated growth model that was already applied to describe the growth dynamics of the parental adherent cell line. In addition, the cellular proteome was analyzed by liquid chromatography coupled to tandem mass spectrometry using a label-free protein quantification method to unravel altered cellular processes for the suspension and the adherent cell line. Four regulatory mechanisms were identified as a response of the adaptation of adherent MDCK cells to growth in suspension. These regulatory mechanisms were linked to the proteins caveolin, cadherin-1, and pirin. Combining cell, metabolite, enzyme, and protein measurements with mathematical modeling generated a more holistic view on cellular processes involved in the adaptation of an adherent cell line to suspension growth. KW - MDCK cell KW - Proteome KW - Metabolism KW - Enzyme activity KW - Suspension growth PY - 2021 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-522070 DO - https://doi.org/10.1007/s00253-021-11150-z VL - 105 IS - 5 SP - 1861 EP - 1874 PB - Springer AN - OPUS4-52207 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Van den Bossche, T. A1 - Verschaffelt, P. A1 - Schallert, K. A1 - Barsnes, H. A1 - Dawyndt, P. A1 - Benndorf, D. A1 - Renard, B. Y. A1 - Mesuere, B. A1 - Martens, L. A1 - Muth, Thilo T1 - Connecting MetaProteomeAnalyzer and PeptideShaker to Unipept for Seamless End-to-End Metaproteomics Data Analysis N2 - Although metaproteomics, the study of the collective proteome of microbial communities, has become increasingly powerful and popular over the past few years, the field has lagged behind on the availability of user-friendly, end-to-end pipelines for data analysis. We therefore describe the Connection from two commonly used metaproteomics data processing tools in the field, MetaProteomeAnalyzer and PeptideShaker, to Unipept for downstream analysis. Through these connections, direct end-to-end pipelines are built from database searching to taxonomic and functional annotation. KW - Metaproteomics KW - Bioinformatics KW - Software KW - Pipelines PY - 2020 DO - https://doi.org/10.1021/acs.jproteome.0c00136 VL - 19 IS - 8 SP - 3562 EP - 3566 PB - ACS Publications AN - OPUS4-51331 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Schiebenhoefer, H. A1 - Schallert, K. A1 - Renard, B. Y. A1 - Trappe, K. A1 - Schmid, E. A1 - Benndorf, D. A1 - Riedel, K. A1 - Muth, Thilo A1 - Fuchs, S. T1 - A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane N2 - Metaproteomics, the study of the collective protein composition of multi-organism systems, provides deep insights into the biodiversity of microbial communities and the complex functional interplay between microbes and their hosts or environment. Thus, metaproteomics has become an indispensable tool in various fields such as microbiology and related medical applications. The computational challenges in the analysis of corresponding datasets differ from those of pure-culture proteomics, e.g., due to the higher complexity of the samples and the larger reference databases demanding specific computing pipelines. Corresponding data analyses usually consist of numerous manual steps that must be closely synchronized. With MetaProteomeAnalyzer and Prophane, we have established two open-source software solutions specifically developed and optimized for metaproteomics. Among other features, peptide-spectrum matching is improved by combining different search engines and, compared to similar tools, metaproteome annotation benefits from the most comprehensive set of available databases (such as NCBI, UniProt, EggNOG, PFAM, and CAZy). The workflow described in this protocol combines both tools and leads the user through the entire data analysis process, including protein database creation, database search, protein grouping and annotation, and results visualization. To the best of our knowledge, this protocol presents the most comprehensive, detailed and flexible guide to metaproteomics data analysis to date. While beginners are provided with robust, easy-to-use, state-of-the-art data analysis in a reasonable time (a few hours, depending on, among other factors, the protein database size and the number of identified peptides and inferred proteins), advanced users benefit from the flexibility and adaptability of the workflow. KW - Bioinformatics KW - Protocol KW - Microbial proteomics KW - Software KW - Mass spectrometry KW - Metaproteomics PY - 2020 DO - https://doi.org/10.1038/s41596-020-0368-7 SN - 1750-2799 VL - 15 IS - 10 SP - 3212 EP - 3239 PB - Nature Publishing Group AN - OPUS4-51335 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -