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Advancing Intact Protein Quantitation with Updated Deconvolution Routines.

Matthew T Robey1,2, Daisha Utley1, Joseph B Greer1,2

  • 1Proteinaceous, Inc., Evanston, Illinois 60201, United States.

Analytical Chemistry
|September 26, 2023
PubMed
Summary

We improved intact protein mass spectrometry analysis by enhancing data processing. Our methods increase detected proteoforms and accuracy, aiding biopharmaceutical and academic research.

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Area of Science:

  • Biochemistry
  • Analytical Chemistry
  • Bioinformatics

Background:

  • Intact protein mass spectrometry is crucial for proteoform quantitation in research.
  • Data analysis presents challenges in mass deconvolution, peak processing, and proteoform matching.
  • Current methods require data-specific parameter tuning, creating informatic hurdles.

Purpose of the Study:

  • To develop improved computational methods for intact protein mass spectrometry data analysis.
  • To enhance the sensitivity, accuracy, and efficiency of proteoform identification and quantitation.
  • To reduce the burden of data analysis for intact mass deconvolution.

Main Methods:

  • Enhanced sliding window mass deconvolution with optimized spectral averaging.
  • Developed a targeted feature-finding routine for increased sensitivity and reproducibility.
  • Improved proteoform annotation using spectral fitting and network viewing.

Main Results:

  • Multiple window averaging increased detected masses by over 2-fold.
  • Targeted feature finding boosted sensitivity over 2-fold and reduced coefficient of variation by 50%.
  • Proteoform annotation methods improved accuracy in identifying related and novel proteoforms.

Conclusions:

  • The developed workflow significantly advances information obtainable from intact protein mass spectrometry.
  • These improvements enhance the quantitation of specific proteoforms in complex biological samples.
  • The refined methods offer a more accurate and efficient approach for proteoform discovery and analysis.