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The Association of Biomolecular Resource Facilities Proteome Informatics Research Group Study on Metaproteomics (iPRG-2020)

Jagtap, Pratik D. (författare)
Hoopmann, Michael R. (författare)
Neely, Benjamin A. (författare)
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Harvey, Antony (författare)
Käll, Lukas, 1969- (författare)
KTH,Genteknologi
Perez-Riverol, Yasset (författare)
European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Trust Genome Campus HinxtonCambridgeCB10 1SD United Kingdom
Abajorga, Milky K. (författare)
Thomas, Julie A. (författare)
Weintraub, Susan T. (författare)
Palmblad, Magnus (författare)
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 (creator_code:org_t)
Association of Biomolecular Resource Facilities, 2023
2023
Engelska.
Ingår i: Journal of biomolecular techniques : JBT. - : Association of Biomolecular Resource Facilities. - 1943-4731. ; 34:3
Relaterad länk:
https://doi.org/10.7...
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https://urn.kb.se/re...
https://doi.org/10.7...
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  • Tidskriftsartikel (refereegranskat)
Abstract Ämnesord
Stäng  
  • Metaproteomics research using mass spectrometry data has emerged as a powerful strategy to understand the mechanisms underlying microbiome dynamics and the interaction of microbiomes with their immediate environment. Recent advances in sample preparation, data acquisition, and bioinformatics workflows have greatly contributed to progress in this field. In 2020, the Association of Biomolecular Research Facilities Proteome Informatics Research Group launched a collaborative study to assess the bioinformatics options available for metaproteomics research. The study was conducted in 2 phases. In the first phase, participants were provided with mass spectrometry data files and were asked to identify the taxonomic composition and relative taxa abundances in the samples without supplying any protein sequence databases. The most challenging question asked of the participants was to postulate the nature of any biological phenomena that may have taken place in the samples, such as interactions among taxonomic species. In the second phase, participants were provided a protein sequence database composed of the species present in the sample and were asked to answer the same set of questions as for phase 1. In this report, we summarize the data processing methods and tools used by participants, including database searching and software tools used for taxonomic and functional analysis. This study provides insights into the status of metaproteomics bioinformatics in participating laboratories and core facilities.

Ämnesord

NATURVETENSKAP  -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
NATURVETENSKAP  -- Data- och informationsvetenskap -- Bioinformatik (hsv//swe)
NATURAL SCIENCES  -- Computer and Information Sciences -- Bioinformatics (hsv//eng)
NATURVETENSKAP  -- Biologi -- Mikrobiologi (hsv//swe)
NATURAL SCIENCES  -- Biological Sciences -- Microbiology (hsv//eng)

Nyckelord

bioinformatics
mass spectrometry
metaproteomics
microbiome
taxonomy

Publikations- och innehållstyp

ref (ämneskategori)
art (ämneskategori)

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