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

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 microbiome. Although it has been useful in develop...

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Detalles Bibliográficos
Autores principales: Miura, Nobuaki, Okuda, Shujiro
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Research Network of Computational and Structural Biotechnology 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9925844/
https://www.ncbi.nlm.nih.gov/pubmed/36817962
http://dx.doi.org/10.1016/j.csbj.2023.01.015
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author Miura, Nobuaki
Okuda, Shujiro
author_facet Miura, Nobuaki
Okuda, Shujiro
author_sort Miura, Nobuaki
collection PubMed
description 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 microbiome. Although it has been useful in developing an understanding of various diseases, its analytical strategies remain limited to the extended application of proteomics. The sequence databases in metaproteomics must be large because of the presence of thousands of species in a typical sample, which causes problems unique to large databases. In this review, we demonstrate the usefulness of metaproteomics in disease research through examples from several studies. Additionally, we discuss the challenges of applying metaproteomics to conventional proteomics analysis methods and introduce studies that may provide clues to the solutions. We also discuss the need for a standard false discovery rate control method for metaproteomics to replace common target-decoy search approaches in proteomics and a method to ensure the reliability of peptide spectrum match.
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spelling pubmed-99258442023-02-16 Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics Miura, Nobuaki Okuda, Shujiro Comput Struct Biotechnol J Review 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 microbiome. Although it has been useful in developing an understanding of various diseases, its analytical strategies remain limited to the extended application of proteomics. The sequence databases in metaproteomics must be large because of the presence of thousands of species in a typical sample, which causes problems unique to large databases. In this review, we demonstrate the usefulness of metaproteomics in disease research through examples from several studies. Additionally, we discuss the challenges of applying metaproteomics to conventional proteomics analysis methods and introduce studies that may provide clues to the solutions. We also discuss the need for a standard false discovery rate control method for metaproteomics to replace common target-decoy search approaches in proteomics and a method to ensure the reliability of peptide spectrum match. Research Network of Computational and Structural Biotechnology 2023-01-16 /pmc/articles/PMC9925844/ /pubmed/36817962 http://dx.doi.org/10.1016/j.csbj.2023.01.015 Text en © 2023 The Author(s) https://creativecommons.org/licenses/by/4.0/This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Miura, Nobuaki
Okuda, Shujiro
Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics
title Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics
title_full Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics
title_fullStr Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics
title_full_unstemmed Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics
title_short Current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics
title_sort current progress and critical challenges to overcome in the bioinformatics of mass spectrometry-based metaproteomics
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9925844/
https://www.ncbi.nlm.nih.gov/pubmed/36817962
http://dx.doi.org/10.1016/j.csbj.2023.01.015
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