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

Abdul Rehman Basharat1, Xingzhao Xiong2, Tian Xu3

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Top-down data-independent acquisition mass spectrometry (TD-DIA-MS) shows promise for identifying more proteoforms. The new TopDIA software tool enables confident proteoform identification using TD-DIA-MS data, outperforming traditional methods.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Computational Biology

Background:

  • Top-down mass spectrometry is crucial for analyzing intact proteoforms.
  • Top-down data-dependent acquisition mass spectrometry (TD-DDA-MS) has been the primary method, but top-down data-independent acquisition mass spectrometry (TD-DIA-MS) remains underexplored.
  • TD-DIA-MS offers potential for increased proteoform identification despite complex spectra.

Approach:

  • Developed TopDIA, the first software for proteoform identification using TD-DIA-MS.
  • TopDIA generates demultiplexed pseudo MS/MS spectra from TD-DIA-MS data.
  • Pseudo MS/MS spectra are searched against protein databases for proteoform identification.

Key Points:

  • TD-DIA-MS, coupled with TopDIA, enhances proteoform and protein identifications.
  • A comparative study using *Escherichia coli* K-12 MG1655 demonstrated the superiority of TD-DIA-MS with TopDIA over TD-DDA-MS.
  • TopDIA effectively addresses the challenge of complex multiplexed spectra in TD-DIA-MS.

Conclusions:

  • TD-DIA-MS represents a significant advancement in proteoform analysis.
  • The TopDIA software tool democratizes the use of TD-DIA-MS for proteoform discovery.
  • This approach expands the scope of proteoform identification and characterization in biological systems.