TY - CHAP A1 - Holstein, Tanja A1 - Muth, Thilo ED - Salerno, C. T1 - Bioinformatic workflows for metaproteomics N2 - The strong influence of microbiomes on areas such as ecology and human health has become widely recognized in the past years. Accordingly, various techniques for the investigation of the composition and function of microbial community samples have been developed. Metaproteomics, the comprehensive analysis of the proteins from microbial communities, allows for the investigation of not only the taxonomy but also the functional and quantitative composition of microbiome samples. Due to the complexity of the investigated communities, methods developed for single organism proteomics cannot be readily applied to metaproteomic samples. For this purpose, methods specifically tailored to metaproteomics are required. In this work, a detailed overview of current bioinformatic solutions and protocols in metaproteomics is given. After an introduction to the proteomic database search, the metaproteomic post-processing steps are explained in detail. Ten specific bioinformatic software solutions are focused on, covering various steps including database-driven identification and quantification as well as taxonomic and functional assignment. KW - Metaproteomics KW - Microbiomes KW - Proteomics KW - Bioinformatic workflow KW - Taxonomic assignment KW - Functional assignment KW - Protein quantification PY - 2024 SN - 978-1-0716-3909-2 SN - 978-1-0716-3910-8 SN - 978-1-0716-3912-2 DO - https://doi.org/10.1007/978-1-0716-3910-8_16 SN - 1064-3745 SN - 1940-6029 N1 - Serientitel: Methods in molecular biology – Series title: Methods in molecular biology VL - 2820 SP - 187 EP - 213 PB - Springer CY - New York, NY AN - OPUS4-62741 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CHAP A1 - Knabe, Nicole A1 - Gorbushina, Anna ED - Gurtler, V. ED - Trevors, J. T. T1 - Territories of rock-inhabiting fungi: Survival on and alteration of solid air-exposed surfaces N2 - Subaerial biofilms that are omnipresent at the interface between all solid substrates and the atmosphere are composed of a unique and widespread group of ascomycetes called rock-inhabiting fungi or microcolonial fungi (MCF), typically in communities with other microorganisms. While subaerial biofilms in toto have important roles in mineral weathering and biodeterioration of materials, methodological approaches to subaerial biofilm communities are diverse and frequently focussed on MCF. Here, we review the historical development of the research methods applied in the field and consider perspectives to increase our understanding of the biofilm-induced changes of solid substrate surfaces. KW - Biologically induced mineral weathering KW - Geobiology KW - Microcolonial fungi KW - Subaerial biofilm KW - Symbiosis PY - 2018 UR - https://linkinghub.elsevier.com/retrieve/pii/S0580951718300047 SN - 9780128146040 DO - https://doi.org/10.1016/bs.mim.2018.06.001 VL - 45 SP - Chapter 6, 145 EP - 169 PB - Elsevier AN - OPUS4-47181 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -