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Selected Reaction Monitoring Mass Spectrometry for Absolute Protein Quantification
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False discovery rate estimation using candidate peptides for each spectrum.

Sangjeong Lee1, Heejin Park1, Hyunwoo Kim2

  • 1Department of Computer Science, Hanyang University, Seoul, 06978, Republic of Korea.

BMC Bioinformatics
|November 2, 2022
PubMed
Summary
This summary is machine-generated.

Accurate false discovery rate (FDR) estimation in proteomics is crucial. A new method, candidate target-decoy strategy (cTDS), improves FDR accuracy by considering differing probabilities of incorrect target or decoy peptide matches.

Keywords:
False discovery rateProteomicsTandem mass spectrometryTarget-decoy strategy

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Computational Biology

Background:

  • False discovery rate (FDR) estimation is critical in proteomics.
  • The standard target-decoy strategy (TDS) assumes equal probabilities for incorrect target and decoy peptide matches, which is often not true.
  • This assumption can lead to inaccurate FDR estimations.

Purpose of the Study:

  • To develop a more accurate method for FDR estimation in proteomics.
  • To introduce the candidate target-decoy strategy (cTDS) that accounts for differing probabilities of incorrect target and decoy peptide matches.

Main Methods:

  • Proposed cTDS (target-decoy strategy with candidate peptides) for FDR estimation.
  • Utilized an entrapment sequence method to validate cTDS accuracy.
  • Compared cTDS performance against TDS using the HEK293 dataset and various decoy databases.

Main Results:

  • Most spectra do not have a 0.5 probability of incorrect target/decoy match; only 1.14-4.85% do.
  • cTDS demonstrated a closer false match rate (FMR) to the target FDR threshold compared to TDS.
  • cTDS identified more peptide-spectrum matches (PSMs) than TDS across multiple replications and decoy strategies at a 1% FDR threshold.

Conclusions:

  • The assumption of identical probabilities for incorrect target and decoy peptide matches in TDS is flawed.
  • cTDS provides a more accurate estimation of FDR by considering the actual probabilities of incorrect matches.
  • cTDS enhances the reliability of peptide identification in proteomics.