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iTop-Q: an Intelligent Tool for Top-down Proteomics Quantitation Using DYAMOND Algorithm.

Hui-Yin Chang1, Ching-Tai Chen1, Chu-Ling Ko2

  • 1Institute of Information Science, Academia Sinica , Taipei 115, Taiwan.

Analytical Chemistry
|November 23, 2017
PubMed
Summary
This summary is machine-generated.

A new tool, iTop-Q, automates proteoform quantitation in top-down proteomics. It uses interspectrum analysis for accurate abundance measurements, improving upon existing methods for analyzing intact proteins.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Biochemistry

Background:

  • Top-down proteomics analyzes intact proteins for genetic variation, splicing, and PTMs.
  • Existing tools struggle with interspectrum quantitation of proteoforms.
  • Automated tools are needed for large-scale proteoform analysis.

Purpose of the Study:

  • To develop an automated tool, iTop-Q, for large-scale proteoform quantitation in top-down proteomics.
  • To enable accurate quantitation across multiple MS1 spectra using interspectrum abundance.
  • To provide a user-friendly solution for complex proteoform analysis.

Main Methods:

  • iTop-Q constructs extracted ion chromatograms (XICs) across adjacent MS1 spectra.
  • It employs the DYAMOND algorithm for dynamic programming-based charge state deconvolution.
  • Proteoform alignment is performed for cross-replicate/sample quantitation.

Main Results:

  • iTop-Q achieves highly accurate and consistent proteoform quantitation.
  • The DYAMOND algorithm effectively handles high charge states and coeluting proteoforms.
  • Performance validated on standard and yeast lysate datasets.

Conclusions:

  • iTop-Q significantly advances automated proteoform quantitation in top-down proteomics.
  • The tool offers improved accuracy and consistency compared to intraspectrum methods.
  • iTop-Q is publicly available, facilitating broader research applications.