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Updated: Jun 5, 2025

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TopDIA: A Software Tool for Top-Down Data-Independent Acquisition Proteomics.

Abdul Rehman Basharat1, Xingzhao Xiong2, Tian Xu3

  • 1Department of BioHealth Informatics, Luddy School of Informatics, Computing and Engineering, Indiana University-Purdue University Indianapolis, Indianapolis, Indiana 46202, United States.

Journal of Proteome Research
|December 6, 2024
PubMed
Summary

Top-down mass spectrometry (MS) is crucial for analyzing intact proteoforms. A new software, TopDIA, enables better proteoform identification using data-independent acquisition MS, outperforming traditional methods.

Keywords:
data independent acquisitionmass spectrometryproteoform identificationtop-down proteomics

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Bioinformatics

Background:

  • Top-down mass spectrometry (MS) is vital for proteoform analysis.
  • Top-down data-dependent acquisition MS (TD-DDA-MS) has historically dominated the field.
  • Top-down data-independent acquisition MS (TD-DIA-MS) remains underexplored despite its potential for broader proteoform coverage.

Purpose of the Study:

  • To introduce TopDIA, the first software tool designed for proteoform identification using TD-DIA-MS.
  • To evaluate the performance of TD-DIA-MS compared to TD-DDA-MS for proteoform discovery.

Main Methods:

  • Development of TopDIA software for processing TD-DIA-MS data.
  • Generation of demultiplexed pseudo MS/MS spectra from TD-DIA-MS raw data.
  • Searching pseudo MS/MS spectra against protein sequence databases for proteoform identification.

Main Results:

  • TD-DIA-MS, coupled with TopDIA, significantly increased the number of identified proteoforms and proteins compared to TD-DDA-MS.
  • The study demonstrated the practical application of TD-DIA-MS for comprehensive proteoform analysis.
  • TopDIA successfully addressed the challenge of complex multiplexed spectra inherent in TD-DIA-MS.

Conclusions:

  • TD-DIA-MS, facilitated by TopDIA, offers a more powerful approach for proteoform identification and characterization.
  • The TopDIA software represents a significant advancement in leveraging TD-DIA-MS for deep proteome analysis.
  • This work expands the utility of top-down mass spectrometry for comprehensive proteoform discovery.