Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial
- Author
- Tim Van Den Bossche (UGent) , Pieter Verschaffelt (UGent) , Tibo Vande Moortele (UGent) , Peter Dawyndt (UGent) , Lennart Martens (UGent) and Bart Mesuere (UGent)
- Organization
- Project
- Abstract
- Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as a valuable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.
- Keywords
- Metaproteomics, Proteomics, Bioinformatics, Biodiversity, Microbiome, Tutorial, Data analysis
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01J471VPQ17VMJFMR798FJM34K
- MLA
- Van Den Bossche, Tim, et al. “Biodiversity Analysis of Metaproteomics Samples with Unipept : A Comprehensive Tutorial.” Protein Bioinformatics, edited by Frédérique Lisacek, vol. 2836, Humana, 2024, pp. 183–215, doi:10.1007/978-1-0716-4007-4_11.
- APA
- Van Den Bossche, T., Verschaffelt, P., Vande Moortele, T., Dawyndt, P., Martens, L., & Mesuere, B. (2024). Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial. In F. Lisacek (Ed.), Protein bioinformatics (Vol. 2836, pp. 183–215). https://doi.org/10.1007/978-1-0716-4007-4_11
- Chicago author-date
- Van Den Bossche, Tim, Pieter Verschaffelt, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, and Bart Mesuere. 2024. “Biodiversity Analysis of Metaproteomics Samples with Unipept : A Comprehensive Tutorial.” In Protein Bioinformatics, edited by Frédérique Lisacek, 2836:183–215. New York, NY: Humana. https://doi.org/10.1007/978-1-0716-4007-4_11.
- Chicago author-date (all authors)
- Van Den Bossche, Tim, Pieter Verschaffelt, Tibo Vande Moortele, Peter Dawyndt, Lennart Martens, and Bart Mesuere. 2024. “Biodiversity Analysis of Metaproteomics Samples with Unipept : A Comprehensive Tutorial.” In Protein Bioinformatics, ed by. Frédérique Lisacek, 2836:183–215. New York, NY: Humana. doi:10.1007/978-1-0716-4007-4_11.
- Vancouver
- 1.Van Den Bossche T, Verschaffelt P, Vande Moortele T, Dawyndt P, Martens L, Mesuere B. Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial. In: Lisacek F, editor. Protein bioinformatics. New York, NY: Humana; 2024. p. 183–215.
- IEEE
- [1]T. Van Den Bossche, P. Verschaffelt, T. Vande Moortele, P. Dawyndt, L. Martens, and B. Mesuere, “Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial,” in Protein bioinformatics, vol. 2836, F. Lisacek, Ed. New York, NY: Humana, 2024, pp. 183–215.
@incollection{01J471VPQ17VMJFMR798FJM34K,
abstract = {{Metaproteomics has become a crucial omics technology for studying microbiomes. In this area, the Unipept ecosystem, accessible at https://unipept.ugent.be, has emerged as a valuable resource for analyzing metaproteomic data. It offers in-depth insights into both taxonomic distributions and functional characteristics of complex ecosystems. This tutorial explains essential concepts like Lowest Common Ancestor (LCA) determination and the handling of peptides with missed cleavages. It also provides a detailed, step-by-step guide on using the Unipept Web application and Unipept Desktop for thorough metaproteomics analyses. By integrating theoretical principles with practical methodologies, this tutorial empowers researchers with the essential knowledge and tools needed to fully utilize metaproteomics in their microbiome studies.}},
author = {{Van Den Bossche, Tim and Verschaffelt, Pieter and Vande Moortele, Tibo and Dawyndt, Peter and Martens, Lennart and Mesuere, Bart}},
booktitle = {{Protein bioinformatics}},
editor = {{Lisacek, Frédérique}},
isbn = {{9781071640067}},
issn = {{1064-3745}},
keywords = {{Metaproteomics,Proteomics,Bioinformatics,Biodiversity,Microbiome,Tutorial,Data analysis}},
language = {{eng}},
pages = {{183--215}},
publisher = {{Humana}},
series = {{Methods in Molecular Biology}},
title = {{Biodiversity analysis of metaproteomics samples with Unipept : a comprehensive tutorial}},
url = {{http://doi.org/10.1007/978-1-0716-4007-4_11}},
volume = {{2836}},
year = {{2024}},
}
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