Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

Using proteomics to mine genome sequences.

Jonathan W Arthur1, Marc R Wilkins

  • 1Proteome Systems Ltd., Locked Bag 2073, North Ryde NSW 1670, Australia. Jonathan.Arthur@proteomesystems.com

Journal of Proteome Research
|July 16, 2004
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

PROTOCOL: Utilisation of Genetics and Genomics in Primary Care: Protocol for an Evidence and Gap Map.

Campbell systematic reviews·2026
Same author

Integrative multiomic analysis reveals co-ordinated alternative splicing in human bone marrow stromal stem cells.

Scientific reports·2026
Same author

Offline Two-Stage SEC and LC-MS/MS for Comprehensive Characterization of Yeast Ribosomal Populations.

Journal of proteome research·2026
Same author

Distinct Enterovirus Antigen Landscape in Children With Islet Autoimmunity.

Diabetes·2026
Same author

WDR5 serves in co-activation and influences genome targeting of KLF3.

Nucleic acids research·2025
Same author

<i>Penicillium psychrofluorescens</i> sp. nov., a naturally autofluorescent Antarctic fungus.

Mycology·2025
Same journal

Proteomic Profiling of Endothelial Cells Under Laminar Shear Stress Confirms the Importance of KLF4 in the Regulation of Membrane Protein Expression Compared to Oscillatory Flow.

Journal of proteome research·2026
Same journal

Identification of Age-Associated Circulating Proteins and Lipids in 3800 Comorbidity-Enriched Older Adults from Japan-Based Cohorts Using Olink Assays and MRM Mass Spectrometry.

Journal of proteome research·2026
Same journal

Molecular Solution to the Paradox of Ancient Brain Preservation.

Journal of proteome research·2026
Same journal

From Method-Defined Signals to Reference Measurement Procedures: Two Decades of Mass Spectrometry-Based ProGRP Quantification.

Journal of proteome research·2026
Same journal

Proteomic Profiling of Extracellular Vesicle-Enriched Plasma Using Mag-Net for Biomarker Discovery in Pancreatic Ductal Adenocarcinoma.

Journal of proteome research·2026
Same journal

Computationally Efficient Bayesian Estimation of Graphical Networks for Omics Data.

Journal of proteome research·2026
See all related articles

This study introduces a novel method to identify protein-coding regions in genomes using mass spectrometry data. It accurately maps genomic sequences to proteins, even without prior annotation.

Area of Science:

  • Genomics
  • Proteomics
  • Bioinformatics

Background:

  • Identifying protein-coding regions in genomes is crucial for understanding biological function.
  • Current methods often rely on pre-existing annotations or specific sequence motifs, limiting their applicability to unannotated or complex genomes.

Purpose of the Study:

  • To develop and validate a computational method for identifying open reading frames (ORFs) in genome sequences using proteomic data.
  • To enable the mining of both annotated and unannotated genomic data for protein-coding regions.

Main Methods:

  • Theoretical translation of genome fragments into virtual proteins in all six reading frames.
  • In silico enzymatic digestion of virtual proteins and comparison of theoretical peptide masses to experimental mass spectrometry data.

Related Experiment Videos

  • Utilizing MALDI-TOF mass spectrometry to analyze peptide masses and identify matching ORFs.

    • Main Results:

    • The method successfully identified coding regions by matching experimental peptide masses to theoretical peptides from virtual proteins.
    • Parameter optimization, including virtual protein size and mass error tolerance, improved detection accuracy.
    • Demonstrated efficacy across diverse organisms, including bacteria (Pseudomonas aeruginosa, Mycobacterium tuberculosis) and eukaryotes (Homo sapiens).

    Conclusions:

    • This proteogenomic approach offers a robust strategy for discovering protein-coding regions in diverse genomes.
    • The method is independent of gene start/stop codon assumptions, enhancing its utility for novel genome analysis.
    • It provides a powerful tool for advancing genome annotation and functional genomics research.