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Related Concept Videos

Proteomics01:33

Proteomics

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A proteome is the entire set of proteins that a cell type produces. We can study proteomes using the knowledge of genomes because genes code for mRNAs, and the mRNAs encode proteins. Although mRNA analysis is a step in the right direction, not all mRNAs are translated into proteins.
Proteomics is the study of proteomes' function. It involves the large-scale systematic study of the proteome to denote the protein complement expressed by a genome. Scientist Mark Wilkins coined the term...
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Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
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Related Experiment Video

Updated: Dec 2, 2025

Label-Free Quantitative Proteomics Workflow for Discovery-Driven Host-Pathogen Interactions
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Modelling of pathogen-host systems using deeper ORF annotations and transcriptomics to inform proteomics analyses.

Sebastien Leblanc1,2, Marie A Brunet1,2

  • 1Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada.

Computational and Structural Biotechnology Journal
|November 2, 2020
PubMed
Summary

This study reveals novel Zika virus interactions by using a customized protein database, identifying previously undiscovered host proteins crucial for understanding Zika virus pathogenicity and developing potential therapeutics.

Keywords:
AP-MS, affinity-purification mass spectrometryAlternative ORFsDEP, differentially expressed proteinsFDR, false discovery rateFPKM, fragments per kilobase of exon model per million reads mappedFlavivirusHCIP, highly confident interacting proteinsHCMV, human cytomegalovirusLFQ, label free quantificationMS, mass spectrometryORF, open reading framePSM, peptide spectrum matchProtein networkProteogenomicsProteome profilingZIKV, Zika virusZikaaltProt, alternative proteinncRNA, non-coding RNAsORF, small open reading frame

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Area of Science:

  • Virology
  • Proteomics
  • Bioinformatics

Background:

  • Zika virus (ZIKV) outbreaks cause severe neurological disorders like microcephaly and Guillain-Barré syndrome.
  • Current treatments are limited, necessitating research into ZIKV pathogenicity and host interactions.
  • Standard protein databases overlook functional proteins due to annotation criteria, potentially missing key viral interactors.

Purpose of the Study:

  • To identify novel human host proteins interacting with Zika virus proteins.
  • To explore the impact of non-annotated proteins on understanding viral pathogenicity.
  • To develop a computational framework for re-analyzing proteomics data in ZIKV infections.

Main Methods:

  • Utilized a customized human protein sequence database excluding minimal open reading frame (ORF) length criteria.
  • Performed protein-protein interaction analysis with ZIKV capsid and NS4A proteins.
  • Conducted proteome profiling of ZIKV-infected monocytes.

Main Results:

  • Identified 4 novel alternative protein interactors for ZIKV capsid and NS4A proteins.
  • Discovered 12 alternative proteins in ZIKV-infected monocytes, with one significantly upregulated.
  • Demonstrated the value of non-annotated proteins in uncovering viral-host interactions.

Conclusions:

  • Customized protein databases enhance the identification of ZIKV-host protein interactions.
  • This approach reveals new potential targets for therapeutic interventions against Zika virus.
  • The proposed computational framework aids in re-analyzing proteomics data for infectious diseases.