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Updated: Sep 21, 2025

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Accurate Proteoform Identification and Quantitation Using pTop 2.0.

Rui-Xiang Sun1,2, Rui-Min Wang3, Lan Luo3

  • 1National Institute of Biological Sciences, Beijing, China. sunruixiang@nibs.ac.cn.

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

pTop 2.0 enhances top-down proteomics by improving the identification and quantification of proteoforms. This advanced bioinformatics tool offers higher accuracy and speed for analyzing complex mass spectrometry data.

Keywords:
Proteoform identification and quantitationSearch engineSemi-supervised learningTandem mass spectrometryTop-down proteomics

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Top-down proteomics has advanced significantly due to technological progress in separation, mass spectrometry (MS), fragmentation, and bioinformatics.
  • Accurate identification and quantification of proteoforms, distinct protein variants from a single gene, remain computationally challenging due to complex mass spectra of intact proteoforms.
  • Existing bioinformatics tools struggle to handle large-scale, complex top-down MS data effectively.

Purpose of the Study:

  • To address the limitations in analyzing complex top-down mass spectrometry data.
  • To introduce pTop 2.0, an enhanced bioinformatics tool for accurate proteoform identification and quantification.
  • To improve the analysis of proteoforms with unexpected modifications or terminal truncations.

Main Methods:

  • Development of pTop 2.0, an upgraded version of the pTop bioinformatics software.
  • Focus on identifying proteoforms with unexpected modifications or terminal truncations.
  • Integration of quantitative analysis using isotopic labeling with a user-friendly 'one-key operation'.

Main Results:

  • pTop 2.0 demonstrates significantly improved accuracy and running speed compared to its predecessor.
  • The software effectively handles complex mass spectra from intact proteoforms.
  • New functionalities include identification of proteoforms with unexpected modifications and isotopic labeling-based quantification.

Conclusions:

  • pTop 2.0 enhances the identification and quantification of intact proteoforms in top-down proteomics.
  • The tool offers a user-friendly interface and improved performance for complex MS data analysis.
  • This advancement pushes the field towards higher accuracy in proteoform analysis.