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Updated: May 9, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
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Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Decoy-free protein-level false discovery rate estimation.

Ben Teng1, Ting Huang, Zengyou He

  • 1School of Software, Dalian University of Technology, Dalian 116621, China.

Bioinformatics (Oxford, England)
|August 9, 2013
PubMed
Summary
This summary is machine-generated.

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This study introduces a novel decoy-free method for estimating the false discovery rate (FDR) in shotgun proteomics. The new approach offers accurate protein identification validation without relying on traditional target-decoy strategies.

Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • Statistical validation is crucial for protein identifications in shotgun proteomics.
  • False discovery rate (FDR) is a key metric for evaluating protein identification results.
  • Existing FDR estimation methods using target-decoy strategies have limitations.

Purpose of the Study:

  • To propose a novel decoy-free method for protein-level FDR estimation.
  • To address the drawbacks of current target-decoy based FDR estimation methods.

Main Methods:

  • Developed a decoy-free FDR estimation method based on permutation P-values under a null hypothesis of random peptide-protein matching.
  • Utilized random bipartite graphs and predicted protein scores via a trained linear regression model to bypass computationally intensive re-inference.

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Last Updated: May 9, 2026

Mapping Dysfunctional Protein-Protein Interactions in Disease
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Mapping Dysfunctional Protein-Protein Interactions in Disease

Published on: October 24, 2025

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification
09:04

Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification

Published on: August 17, 2015

  • Calculated FDR using permutation P-values derived from predicted scores on shuffled graphs.

    • Main Results:

    • The proposed method was tested on six public datasets.
    • Decoy-free FDR estimation accuracy was comparable to state-of-the-art algorithms.
    • The method provides a viable alternative to target-decoy strategies.

    Conclusions:

    • The new decoy-free method effectively estimates protein-level FDR.
    • This approach offers a computationally efficient and accurate alternative for validating protein identifications in shotgun proteomics.
    • The source code is publicly available for use and further development.