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The microbiologist's guide to metaproteomics [PDF]

iMeta
Metaproteomics is an emerging approach for studying microbiomes, offering the ability to characterize proteins that underpin microbial functionality within diverse ecosystems.
Lucia Grenga, Sérgio Uzzau, Timothy Griffin   +2 more
exaly   +15 more sources

iMetaLab Suite: A one‐stop toolset for metaproteomics

iMeta, 2022
Metaproteomics is a recently thriving technique that studies the collection of proteins in complex microbiomes of the human, animal, plant, and environment.
Caitlin Simopoulos, Daniel Figeys, Kai Cheng   +2 more
exaly   +3 more sources

The Metaproteomics Initiative: five years of community-driven progress [PDF]

Microbiome
The Metaproteomics Initiative was officially launched in 2021 to strengthen collaboration, promote knowledge exchange, and support and lead standardization efforts within the growing metaproteomics community.
Tim Van Den Bossche, Lucia Grenga, Gelio Alves, Magnus Ø. Arntzen, Dirk Benndorf, Madita Brauer, Daniel Figeys, Celine Henry, Robert L. Hettich, Robert Heyer, Pratik D. Jagtap, Nico Jehmlich, Manuel Kleiner, Leyuan Li, Bart Mesuere, Martin Pabst, Jagroop Pandhal, Phillip B. Pope, Jana Seifert, Anke Trautwein-Schult, Pieter Verschaffelt, Paul Wilmes, Jean Armengaud, Benoit J. Kunath   +23 more
doaj   +3 more sources

Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics

Computational and Structural Biotechnology Journal, 2023
Metaproteomics is a relatively young field that has only been studied for approximately 15 years. Nevertheless, it has the potential to play a key role in disease research by elucidating the mechanisms of communication between the human host and the ...
Shujiro Okuda
exaly   +3 more sources

MetaPep: A core peptide database for faster human gut metaproteomics database searches

Computational and Structural Biotechnology Journal, 2023
Metaproteomics has increasingly been applied to study functional changes in the human gut microbiome. Peptide identification is an important step in metaproteomics research, with sequence database search (SDS) and spectral library search (SLS) as the two
Zhongzhi Sun, Zhibin Ning, Kai Cheng, Haonan Duan, Qing Wu, Janice Mayne, Daniel Figeys   +6 more
doaj   +2 more sources

The need for standardization and improved open (meta)data practices in metaproteomics [PDF]

Microbiome
Metaproteomics enables functional insight into microbial communities by identifying and quantifying proteins in complex samples. Yet, heterogeneous analytical workflows and the lack of standardization across experimental and bioinformatics stages hinder ...
Tim Van Den Bossche, Maximilian Wolf, Jean Armengaud, Magnus Ø. Arntzen, Dirk Benndorf, Daniel Figeys, Lucia Grenga, Robert L. Hettich, Nithu Sara John, Pratik Jagtap, Nico Jehmlich, Manuel Kleiner, Benoit J. Kunath, Leyuan Li, Mary Lipton, Bart Mesuere, Benjamin A. Neely, Zhibin Ning, Ane Laura Pedersen, Yasset Perez-Riverol, Jeena Rajan, Kay Schallert, Jana Seifert, Sergio Uzzau, Pieter Verschaffelt, Paul Wilmes, Juan Antonio Vizcaíno, Lennart Martens, Robert Heyer   +28 more
doaj   +2 more sources

Systematic evaluation of PASEF acquisition strategies in complex metaproteomes [PDF]

Nature Communications
Metaproteomics measures functional expression in complex microbial communities, but extreme sample complexity and dynamic range challenge acquisition strategies.
Feng Xian, Goran Mitulovic, Ranjith Kumar Ravi Kumar, Lukas Uhrik, Elisabeth Urbauer, Doriane Aguanno, Dirk Haller, Manuela Schmidt, David Gomez-Varela   +8 more
doaj   +2 more sources

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes

Microbiome, 2021
Through connecting genomic and metabolic information, metaproteomics is an essential approach for understanding how microbiomes function in space and time.
Tim Van Den Bossche, Magnus Ø. Arntzen, Dörte Becher, Dirk Benndorf, Vincent G. H. Eijsink, Céline Henry, Pratik D. Jagtap, Nico Jehmlich, Catherine Juste, Benoit J. Kunath, Bart Mesuere, Thilo Muth, Phillip B. Pope, Jana Seifert, Alessandro Tanca, Sergio Uzzau, Paul Wilmes, Robert L. Hettich, Jean Armengaud   +18 more
doaj   +1 more source

Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota

npj Biofilms and Microbiomes, 2023
Metaproteomics can provide valuable insights into the functions of human gut microbiota (GM), but is challenging due to the extreme complexity and heterogeneity of GM.
Jinzhi Zhao, Yi Yang, Hua Xu, Jianxujie Zheng, Chengpin Shen, Tian Chen, Tao Wang, Bing Wang, Jia Yi, Dan Zhao, Enhui Wu, Qin Qin, Li Xia, Liang Qiao   +13 more
doaj   +1 more source

In-Depth Metaproteomics Analysis of Oral Microbiome for Lung Cancer

Research, 2022
The human oral microbiome correlates with numerous diseases, including lung cancer. Identifying the functional changes by metaproteomics helps understand the disease-related dysbiosis, yet characterizing low-abundant bacteria is challenging.
Xiaoteng Jiang, Yan Zhang, Huiyu Wang, Zeyuan Wang, Shen Hu, Chengxi Cao, Hua Xiao   +6 more
doaj   +1 more source