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Linear and Differential Ion Mobility Separations of Middle-Down Proteoforms.

Alyssa Garabedian1, Matthew A Baird2, Jacob Porter1

  • 1Department of Chemistry and Biochemistry, Florida International University , Miami, Florida 33199, United States.

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|January 24, 2018
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High-resolution linear ion mobility spectrometry (IMS) can now separate complex proteoforms, like histone tails with various post-translational modifications (PTMs). This advance enables more comprehensive proteome characterization using mass spectrometry (MS).

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Characterizing proteomes with identical proteins but different post-translational modifications (PTMs) is challenging.
  • Proteoform isomers often require separation before mass spectrometric analysis, but conventional methods are insufficient for their size.
  • Differential ion mobility spectrometry (FAIMS) has resolved some variants, but linear ion mobility spectrometry (IMS) has not been effective for absolute mobility-based separation.

Purpose of the Study:

  • To demonstrate the capability of high-resolution linear IMS for separating proteoform variants.
  • To assess the transferability of separation results across different linear IMS instruments.
  • To evaluate the orthogonality of linear IMS and FAIMS for enhanced proteoform analysis.

Main Methods:

  • Utilized trapped ion mobility spectrometry (TIMS), a high-resolution linear IMS technique.
  • Employed complete histone tails with diverse PTMs on alternative sites as model proteoforms.
  • Performed separations across various charge states and analyzed mixtures using tandem mass spectrometry (MS/MS).

Main Results:

  • High-resolution linear IMS (specifically TIMS) effectively resolved proteoform variants of approximately 50 residues.
  • Separation performance was similar across different linear IMS instruments (TIMS, TWIMS) and conditions, indicating result transferability.
  • Linear IMS and FAIMS demonstrated substantially orthogonal separation dimensions.

Conclusions:

  • High-resolution linear IMS is a powerful tool for resolving complex proteoform isomers, including those with PTMs.
  • The orthogonality of linear IMS and FAIMS suggests a combined FAIMS/IMS/MS platform for advanced proteome characterization.
  • This approach significantly advances the comprehensive analysis of proteoforms.