PepMANDIS: A Peptide Selection Tool for Designing Function-Based Targeted Proteomic Assays in Complex Microbial Systems.
LC-MS/MS
bioinformatics tool
environmental proteomics
in silico peptide selection
microbial ecology
microbial functioning
targeted metaproteomics
Journal
Frontiers in chemistry
ISSN: 2296-2646
Titre abrégé: Front Chem
Pays: Switzerland
ID NLM: 101627988
Informations de publication
Date de publication:
2021
2021
Historique:
received:
08
06
2021
accepted:
02
08
2021
entrez:
7
9
2021
pubmed:
8
9
2021
medline:
8
9
2021
Statut:
epublish
Résumé
The majority of studies focusing on microbial functioning in various environments are based on DNA or RNA sequencing techniques that have inherent limitations and usually provide a distorted picture about the functional status of the studied system. Untargeted proteomics is better suited for that purpose, but it suffers from low efficiency when applied in complex consortia. In practice, the scanning capabilities of the currently employed LC-MS/MS systems provide limited coverage of key-acting proteins, hardly allowing a semiquantitative assessment of the most abundant ones from most prevalent species. When particular biological processes of high importance are under investigation, the analysis of specific proteins using targeted proteomics is a more appropriate strategy as it offers superior sensitivity and comes with the added benefits of increased throughput, dynamic range and selectivity. However, the development of targeted assays requires
Identifiants
pubmed: 34490209
doi: 10.3389/fchem.2021.722087
pii: 722087
pmc: PMC8416534
doi:
Types de publication
Journal Article
Langues
eng
Pagination
722087Informations de copyright
Copyright © 2021 Medvecky and Mandalakis.
Déclaration de conflit d'intérêts
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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