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Neutron-encoded mass signatures for quantitative top-down proteomics.

Timothy W Rhoads1, Christopher M Rose, Derek J Bailey

  • 1Department of Chemistry, ‡Department of Biomolecular Chemistry, §Genome Center, and ∇Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States.

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We adapted NeuCode Stable Isotope Labeling by Amino acids in Cell culture (SILAC) for intact proteins, enabling accurate quantitative proteomics in top-down experiments. This method uses high-resolution mass spectrometry for robust protein identification and quantification.

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Area of Science:

  • Proteomics
  • Analytical Chemistry
  • Biochemistry

Background:

  • Quantitative proteomics is crucial for understanding biological systems.
  • Existing methods like shotgun and top-down proteomics require accurate quantitation strategies.
  • Stable Isotope Labeling by Amino acids in Cell culture (SILAC) is a powerful tool for quantitative proteomics.

Purpose of the Study:

  • To extend the NeuCode SILAC quantitation strategy to intact proteins for top-down proteomics.
  • To enable robust, multiplexed quantitation of proteins using high-resolution mass spectrometry.
  • To leverage the unique properties of NeuCode SILAC for protein identification and quantification.

Main Methods:

  • Utilized yeast lysate labeled with isotopologues of lysine ((13)C6(15)N2-lysine or (2)H8-lysine) with a mass difference of 36 mDa.
  • Employed high-resolution mass spectrometry to resolve and quantify the closely spaced isotope-labeled proteins.
  • Performed MS(2)-based quantitation using Electron Transfer Dissociation (ETD).

Main Results:

  • Successfully quantified several hundred isotope distributions in top-down proteomics experiments.
  • Demonstrated accurate protein identification and quantification across various mixed ratios (1:1, 3:1, 5:1).
  • Showcased the utility of isotope peak spacing for determining the number of lysines, aiding protein identification.

Conclusions:

  • NeuCode SILAC is applicable to intact proteins, providing a robust method for quantitative top-down proteomics.
  • The technique offers high accuracy and multiplexing capabilities for protein analysis.
  • This advancement enhances protein identification and quantification in complex biological samples.