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

Confident protein identification using the average peptide score method coupled with search-specific, ab initio

Ian Shadforth1, Tom Dunkley, Kathryn Lilley

  • 1Department of Analytical Science and Informatics, Cranfield University at Silsoe, Befordshire, UK. i.p.shadforth.s01@cranfield.ac.uk

Rapid Communications in Mass Spectrometry : RCM
|October 20, 2005
PubMed
Summary

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

Occurrence, patterns and previously overlooked sources of three veterinary ectoparasiticides in rural and urban Welsh rivers.

Environmental pollution (Barking, Essex : 1987)·2026
Same author

Clinical validation of a machine-learned, point-of-care system to IDENTIFY pulmonary hypertension.

ERJ open research·2025
Same author

Facilitating Earlier Diagnosis of Pulmonary Hypertension Using a Novel Noninvasive Diagnostic.

JACC. Case reports·2025
Same author

Understanding the sources of performance in deep drug response models reveals insights and improvements.

Bioinformatics (Oxford, England)·2025
Same author

Redox-regulated Aux/IAA multimerization modulates auxin responses.

Science (New York, N.Y.)·2025
Same author

Signal Acquisition, Score Interpretation, and Economics of a Non-Invasive Point-of-Care Test for Coronary Artery Disease.

Journal of visualized experiments : JoVE·2024

This study introduces a new scoring strategy for mass spectrometry protein identifications, enhancing confidence and minimizing false positives. The method combines Average Peptide Score (APS) with peptide quality filtering for reliable results without needing known datasets.

Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Interpreting mass spectrometry data for protein identification is challenging due to potential false positives.
  • Standard significance thresholds (e.g., 95%) are insufficient for high-confidence protein identification in large datasets.

Purpose of the Study:

  • To develop an innovative scoring strategy for increasing confidence in protein identifications from mass spectrometry.
  • To minimize false-positive protein identifications without relying on external validation datasets.

Main Methods:

  • Coupling the Average Peptide Score (APS) method with a pre-filtering strategy for peptide identifications.
  • Utilizing iterative generation of peptide quality filters and reversed database searching to set optimal thresholds.

Related Experiment Videos

  • Establishing thresholds for APS and peptide quality to achieve virtually zero false-positive reports.

    • Main Results:

    • The developed scoring strategy significantly enhances the confidence of protein identifications.
    • The method effectively reduces false-positive reports to near zero.
    • Achieved high-confidence results without the need for a known dataset for validation.

    Conclusions:

    • The novel scoring strategy provides a robust approach for reliable protein identification in mass spectrometry.
    • This method offers a significant improvement over existing techniques for managing false positives.
    • The approach is valuable for researchers working with large-scale proteomics data.