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Method for Independent Estimation of the False Localization Rate for Phosphoproteomics.

Kerry A Ramsbottom1, Ananth Prakash2, Yasset Perez Riverol2

  • 1Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool L69 3BX, U.K.

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|May 31, 2022
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Summary

This study introduces a novel decoy amino acid method to accurately estimate the global false localization rate (FLR) in phosphoproteomic data. Using alanine and leucine as decoys provides reliable FLR assessment, improving data accuracy.

Keywords:
database searchingfalse localization ratephosphoproteomicssoftwarestatistics

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Area of Science:

  • Proteomics
  • Biochemistry
  • Bioinformatics

Background:

  • Phosphoproteomic methods identify protein phosphorylation sites.
  • Current tools estimate global false localization rate (FLR) but lack validation on real datasets.
  • This can lead to reporting of incorrectly localized phosphosites.

Purpose of the Study:

  • To develop a novel method for independent estimation of global FLR in phosphoproteomics.
  • To assess the reliability of different decoy amino acids for FLR estimation.
  • To improve the accuracy of phosphosite identification and reporting.

Main Methods:

  • Developed a concept of scoring modifications on decoy amino acids (non-modifiable).
  • Tested various amino acids on synthetic and real phosphoproteomic datasets.
  • Evaluated the impact of decoy selection on global FLR estimation.

Main Results:

  • Decoy amino acid selection significantly impacts estimated global FLR.
  • Alanine and leucine decoys yielded the most reliable FLR results.
  • The method allows for independent estimation of global FLR.

Conclusions:

  • Decoy amino acids offer a robust approach to control false reporting in phosphoproteomics.
  • Using alanine or leucine as decoys enhances the statistical reliability of FLR.
  • This method is proposed for controlling false positives in literature and public databases.