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Updated: Sep 21, 2025

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Proteoform Identification and Quantification Using Intact Protein Database Search Engine ProteinGoggle.

Suideng Qin1, Zhixin Tian2

  • 1School of Chemical Science & Engineering and Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, Shanghai, China.

Methods in Molecular Biology (Clifton, N.J.)
|June 3, 2022
PubMed
Summary

Top-down proteomics uses mass spectrometry to analyze intact proteins, identifying sequences and modifications. This approach aids in understanding protein function and disease, with new algorithms like "isotopic mass-to-charge ratio and envelope fingerprinting" enhancing protein identification.

Keywords:
Cross-talkIdentificationLocalizationPosttranslational modificationProteoformQuantification

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Proteomics investigates protein expression differences in physiological or pathological states.
  • Identifying protein sequences and post-translational modifications (PTMs) is crucial for understanding proteoform structure and function.
  • Advancements in soft ionization techniques and high-resolution mass spectrometers have enabled top-down proteomics.

Purpose of the Study:

  • To provide an overview of top-down proteomics.
  • To introduce the "isotopic mass-to-charge ratio and envelope fingerprinting" algorithm for intact protein database searching.
  • To present the ProteinGoggle search engine.

Main Methods:

  • Utilizing mass spectrometry (MS) for intact protein characterization.
  • Employing soft ionization technologies like electrospray ionization.
  • Developing and applying database search algorithms for protein identification.

Main Results:

  • Top-down proteomics allows for the comprehensive analysis of complete proteins.
  • The "isotopic mass-to-charge ratio and envelope fingerprinting" algorithm facilitates accurate protein identification.
  • The ProteinGoggle search engine is a tool for protein identification in proteomics studies.

Conclusions:

  • Top-down proteomics is a valuable approach for systematic understanding of proteoforms.
  • Advanced MS techniques and bioinformatics tools are essential for modern proteomics.
  • The discussed algorithm and search engine contribute to improved protein identification capabilities.