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Improved False Discovery Rate Estimation Procedure for Shotgun Proteomics.

Uri Keich¹, Attila Kertesz-Farkas², William Stafford Noble^2,3

¹†School of Mathematics and Statistics F07, University of Sydney, Sydney, New South Wales 2006, Australia.

Journal of Proteome Research

|July 9, 2015

Summary

Related Concept Videos

Peptide Identification Using Tandem Mass Spectrometry

Peptide Identification Using Tandem Mass Spectrometry

Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
This technique helps gather information regarding the protein from which the peptide was obtained and to study the peptides’ amino acid sequence. Identifying peptides from a complex mixture is an important component of the growing field of...

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Accurate statistical confidence estimation is vital for shotgun proteomics. This study introduces the mix-max procedure for unbiased false discovery rate (FDR) estimation, improving upon existing target-decoy methods.

Area of Science:

Proteomics
Bioinformatics
Computational Biology

Background:

Shotgun proteomics generates numerous hypotheses requiring statistical confidence estimates for identified tandem mass spectra.
Current methods for estimating false discovery rate (FDR) lack scientific consensus, impacting high-throughput proteomics data interpretation.
Existing protocols, including target-decoy competition (TDC) and separate target-decoy searches, have limitations in accuracy and data retention.

Purpose of the Study:

To evaluate and compare the accuracy of existing FDR estimation protocols in proteomics.
To identify biases and limitations in current target-decoy strategies for mass spectrometry data.
To propose a novel, unbiased method for FDR estimation in proteomics.

Main Methods:

Keywords:

false discovery rate mass spectrometry spectrum identification

Related Experiment Videos

Theoretical and empirical analysis of four established FDR estimation protocols.

Evaluation of two variants of the target-decoy competition (TDC) protocol.

Assessment of two variants of the separate target-decoy search protocol.

Development and validation of the proposed mix-max procedure.

Main Results:

Significant biases were identified in the separate target-decoy search protocols.
The most accurate TDC protocol resulted in the forfeiture of high-scoring spectrum identifications.
The proposed mix-max procedure demonstrated unbiased and accurate FDR estimation.
The mix-max procedure avoids biases of separate searches and data loss from TDC.

Conclusions:

Existing FDR estimation methods in proteomics have inherent biases and limitations.
The novel mix-max procedure offers an unbiased and accurate approach to FDR estimation.
This method improves confidence in identified tandem mass spectra, enhancing proteomics data reliability.