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Quetzal: Comprehensive Peptide Fragmentation Annotation and Visualization.

Eric W Deutsch1, Luis Mendoza1, Robert L Moritz1

  • 1Institute for Systems Biology, Seattle, Washington 98109, United States.

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|March 20, 2025
PubMed
Summary

Researchers can use Quetzal, a new tool, to verify critical peptide-spectrum matches in proteomics data. This ensures the accuracy of study conclusions derived from high-resolution mass spectrometry analyses.

Keywords:
QuetzalUniversal Spectrum Identifiermass spectrometrymzPAFproteomicsspectrum annotation

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • High-resolution mass spectrometry (MS) in proteomics generates high-quality data but includes incorrect identifications due to false discovery rate (FDR) thresholding.
  • Ensuring the accuracy of peptide-spectrum matches (PSMs) is crucial for study conclusions, especially when relying on a limited number of correct identifications.

Purpose of the Study:

  • To introduce Quetzal, a novel peptide fragment ion spectrum annotation tool.
  • To assist researchers in annotating and examining spectra for validation of crucial PSMs.
  • To ensure that spectral evidence correctly supports study conclusions in proteomics research.

Main Methods:

  • Quetzal annotates spectra utilizing the Human Proteome Organization (HUPO) Proteomics Standards Initiative (PSI) mzPAF standard for fragment ion peak annotation.
  • The tool is implemented with Python-based code and offers a web-service endpoint for annotation services.
  • A web-based application is provided for interactive spectrum annotation and generation of publication-quality figures.

Main Results:

  • Demonstrated Quetzal's functionality through the annotation of diverse spectra, showcasing its capability with varying complexity.
  • Highlighted the tool's role in validating the correctness of PSMs, thereby increasing confidence in proteomics data interpretation.
  • Confirmed the accessibility and utility of Quetzal for researchers needing to verify critical spectral evidence.

Conclusions:

  • Quetzal offers accessible functionality to aid researchers in ensuring and demonstrating that crucial spectra accurately support study conclusions.
  • The tool facilitates rigorous validation of MS data, enhancing the reliability of proteomics-based scientific findings.
  • Quetzal is publicly available, promoting its adoption in the proteomics community for improved data quality assurance.