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Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in

Honglan Li1, Jonghun Park2, Hyunwoo Kim3

  • 1School of Computer Science and Engineering, Soongsil University , Seoul 06978, Republic of Korea.

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|April 29, 2017
PubMed
Summary

Proteogenomic searches identify novel peptides using tandem mass spectrometry. Mixture model-based methods with separate false discovery rate (FDR) control offer the most sensitive and reliable novel peptide identification.

Keywords:
false discovery rate controlnovel peptide identificationproteogenomic searchsimulationspike-in data

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Area of Science:

  • Proteomics
  • Bioinformatics
  • Mass Spectrometry

Background:

  • Proteogenomic searches are crucial for identifying novel peptides from mass spectrometry data.
  • Accurate control of the false discovery rate (FDR) is essential for reliable proteogenomic analysis.
  • Previous evaluations of FDR control methods for novel peptide identification are limited.

Purpose of the Study:

  • To evaluate the performance of different false discovery rate (FDR) control methods in proteogenomic searches.
  • To compare the sensitivity and accuracy of global, separate, and multistage FDR estimation approaches.
  • To determine the optimal FDR control strategy for sensitive and reliable novel peptide identification.

Main Methods:

  • Simulated proteogenomic searches using a controlled, spike-in dataset.
  • Validation of simulation approach using a real human cell line dataset.
  • Evaluation of six FDR control methods: global, separate, and multistage FDR estimation, coupled with target-decoy search and mixture model-based methods.

Main Results:

  • The multistage approach demonstrated the highest accuracy in FDR estimation.
  • Global and separate FDR estimation using the mixture model-based method achieved higher sensitivity at the same true FDR.
  • The mixture model-based method performed robustly with or without reduced decoy sequences.

Conclusions:

  • Mixture model-based methods with separate FDR estimation are recommended for sensitive and reliable novel peptide identification in proteogenomic searches.
  • The choice of FDR control method impacts the trade-off between accuracy and sensitivity.
  • This study provides a framework for optimizing proteogenomic data analysis.