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An Integrated Workflow of Identification and Quantification on FDR Control-Based Untargeted Metabolome

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Target-decoy approach and false discovery rate: when things may go wrong.

Nitin Gupta¹, Nuno Bandeira, Uri Keich

¹Bioinformatics Program, University of California San Diego, La Jolla, CA, USA.

Journal of the American Society for Mass Spectrometry

|September 29, 2011

Summary

The target-decoy approach (TDA) for proteomics needs re-evaluation. While useful for estimating false discovery rates (FDR), its limitations and non-compliant tools necessitate a critical review for accurate peptide identification.

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Area of Science:

Proteomics
Computational Biology
Mass Spectrometry

Background:

The target-decoy approach (TDA) is widely used in proteomics to estimate false discovery rates (FDR) for peptide identifications.
TDA has been instrumental in establishing confidence levels for peptide-spectrum matches (PSMs) in mass spectrometry-based proteomics.
Despite its utility, TDA has inherent limitations and potential drawbacks that warrant critical examination.

Purpose of the Study:

To critically re-examine the target-decoy approach (TDA) in proteomics, highlighting both its merits and demerits.
To investigate the compliance of popular MS/MS search tools with TDA principles.
To propose alternatives or improvements for FDR estimation in proteomics.

Main Methods:

Analysis of existing target-decoy approach (TDA) methodologies and their theoretical underpinnings.
Evaluation of popular MS/MS search tools for TDA compliance.
Development and comparison of non-TDA compliant tools against TDA-compliant ones.
Assessment of the impact of the 'coin toss' factor in TDA-based FDR estimation.

Main Results:

Demonstrated that some widely used MS/MS search tools are not compliant with the target-decoy approach (TDA).
Showcased the development of non-TDA compliant tools that outperform TDA-compliant tools in performance.
Identified concerns regarding the reliance of TDA on a probabilistic 'coin toss' for FDR estimation.
Highlighted the difficulty in distinguishing between TDA-compliant and non-TDA compliant tools.

Conclusions:

The target-decoy approach (TDA) is not a universal solution and has limitations that require critical re-evaluation.
The proliferation of non-TDA compliant tools is a concern due to the elusiveness of compliance criteria.
Accurate p-values for individual peptide-spectrum matches (PSMs) can potentially eliminate the need for TDA in FDR estimation.