Metaproteomics: Methods and Protocols

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The Unipept metaproteomics analysis pipeline von Mesuere, Bart, Debyser, Griet, Aerts, Maarten, Devreese, Bart, Vandamme, Peter, Dawyndt, Peter

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Data-Independent Acquisition Mass Spectrometry in Metaproteomics of Gut MicrobiotaImplementation and Computational Analysis von Aakko, Juhani, Pietilä, Sami, Suomi, Tomi, Mahmoudian, Mehrad, Toivonen, Raine, Kouvonen, Petri, Rokka, Anne, Hänninen, Arno, Elo, Laura L

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Soil metaproteomics – Comparative evaluation of protein extraction protocols von Keiblinger, Katharina M., Wilhartitz, Inés C., Schneider, Thomas, Roschitzki, Bernd, Schmid, Emanuel, Eberl, Leo, Riedel, Kathrin, Zechmeister-Boltenstern, Sophie

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Assessing species biomass contributions in microbial communities via metaproteomics von Kleiner, Manuel, Thorson, Erin, Sharp, Christine E., Dong, Xiaoli, Liu, Dan, Li, Carmen, Strous, Marc

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Navigating through metaproteomics data: A logbook of database searching von Muth, Thilo, Kolmeder, Carolin A., Salojärvi, Jarkko, Keskitalo, Salla, Varjosalo, Markku, Verdam, Froukje J., Rensen, Sander S., Reichl, Udo, de Vos, Willem M., Rapp, Erdmann, Martens, Lennart

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Who is who in litter decomposition? Metaproteomics reveals major microbial players and their biogeochemical functions von Schneider, Thomas, Keiblinger, Katharina M, Schmid, Emanuel, Sterflinger-Gleixner, Katja, Ellersdorfer, Günther, Roschitzki, Bernd, Richter, Andreas, Eberl, Leo, Zechmeister-Boltenstern, Sophie, Riedel, Kathrin

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MetaFS: Performance assessment of biomarker discovery in metaproteomics von Tang, Jing, Mou, Minjie, Wang, Yunxia, Luo, Yongchao, Zhu, Feng

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Proteomics of Communities: Metaproteomics von Yates, 3rd, John R

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Metaproteomics Analysis of Host–Microbiota Interfaces von van der Post, Sjoerd, Arike, Liisa

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Distinct gut metagenomics and metaproteomics signatures in prediabetics and treatment-naïve type 2 diabetics von Zhong, Huanzi, Ren, Huahui, Lu, Yan, Fang, Chao, Hou, Guixue, Yang, Ziyi, Chen, Bing, Yang, Fangming, Zhao, Yue, Shi, Zhun, Zhou, Baojin, Wu, Jiegen, Zou, Hua, Zi, Jin, Chen, Jiayu, Bao, Xiao, Hu, Yihe, Gao, Yan, Zhang, Jun, Xu, Xun, Hou, Yong, Yang, Huanming, Wang, Jian, Liu, Siqi, Jia, Huijue, Madsen, Lise, Brix, Susanne, Kristiansen, Karsten, Liu, Fang, Li, Junhua

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Perspective and Guidelines for Metaproteomics in Microbiome Studies von Zhang, Xu, Figeys, Daniel

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Critical steps in an environmental metaproteomics workflow von Nebauer, Daniel J., Pearson, Leanne A., Neilan, Brett A.

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Metaproteomics reveals associations between microbiome and intestinal extracellular vesicle proteins in pediatric inflammatory bowel disease von Zhang, Xu, Deeke, Shelley A., Ning, Zhibin, Starr, Amanda E., Butcher, James, Li, Jennifer, Mayne, Janice, Cheng, Kai, Liao, Bo, Li, Leyuan, Singleton, Ruth, Mack, David, Stintzi, Alain, Figeys, Daniel

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Enhancing metaproteomics-The value of models and defined environmental microbial systems von Herbst, Florian-Alexander, Lünsmann, Vanessa, Kjeldal, Henrik, Jehmlich, Nico, Tholey, Andreas, von Bergen, Martin, Nielsen, Jeppe Lund, Hettich, Robert L., Seifert, Jana, Nielsen, Per Halkjær

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Metaproteomics of Gut Fungi in Gnotobiotic Mice von Pettersen, Veronika Kuchařová

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Comparative metaproteomics analysis shows altered fecal microbiota signatures in patients with major depressive disorder von Chen, Zhi, Li, Jie, Gui, Siwen, Zhou, Chanjuan, Chen, Jianjun, Yang, Chuangchuang, Hu, Zicheng, Wang, Haiyang, Zhong, Xiaogang, Zeng, Li, Chen, Ke, Li, Pengfei, Xie, Peng

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Deep Metaproteomics Approach for the Study of Human Microbiomes von Zhang, Xu, Chen, Wendong, Ning, Zhibin, Mayne, Janice, Mack, David, Stintzi, Alain, Tian, Ruijun, Figeys, Daniel

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Survey of metaproteomics software tools for functional microbiome analysis von Sajulga, Ray, Easterly, Caleb, Riffle, Michael, Mesuere, Bart, Muth, Thilo, Mehta, Subina, Kumar, Praveen, Johnson, James, Gruening, Bjoern Andreas, Schiebenhoefer, Henning, Kolmeder, Carolin A, Fuchs, Stephan, Nunn, Brook L, Rudney, Joel, Griffin, Timothy J, Jagtap, Pratik D

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Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics von Bergauer, Kristin, Fernandez-Guerra, Antonio, Garcia, Juan A. L., Sprenger, Richard R., Stepanauskas, Ramunas, Pachiadaki, Maria G., Jensen, Ole N., Herndl, Gerhard J.

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