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Multiplexed quantification for data-independent acquisition.

Catherine E Minogue1, Alexander S Hebert, Jarred W Rensvold

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

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|January 27, 2015
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Summary
This summary is machine-generated.

We developed NeuCode SILAC for data-independent acquisition (NeuCoDIA), enabling multiplexed quantitative proteomic analysis. This method offers accurate and precise results comparable to existing techniques for biological studies.

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Quantitative Biology

Background:

  • Data-independent acquisition (DIA) offers sensitive and reproducible proteomic analysis.
  • DIA is incompatible with common multiplexed quantification methods like stable isotope labeling.
  • Stable isotope labeling of amino acids in cell culture (SILAC) is a widely used quantitative method.

Purpose of the Study:

  • To expand the use of neutron-encoded (NeuCode) SILAC to DIA applications.
  • To develop a strategy enabling multiplexing within DIA scans without complicating MS(2) spectra.
  • To establish DIA quantification of NeuCode SILAC as a practical alternative to data-dependent acquisition (DDA).

Main Methods:

  • Developed NeuCode SILAC for DIA (NeuCoDIA).
  • Performed duplex NeuCoDIA analysis on mixed-ratio yeast and mouse embryo myogenesis proteomes.
  • Quantified proteomic changes using MS(1)-based and NeuCoDIA approaches.

Main Results:

  • NeuCoDIA demonstrated high accuracy and precision in mixed-ratio yeast samples, comparable to MS(1)-based quantification.
  • The method successfully uncovered dynamic protein changes during mouse myogenic differentiation.
  • NeuCoDIA enables multiplexing within DIA scans without increased spectral complexity.

Conclusions:

  • NeuCoDIA is a feasible and practical methodology for large-scale quantitative proteomic analyses.
  • This approach overcomes the incompatibility of DIA with SILAC-based multiplexing.
  • NeuCoDIA provides a valuable alternative to DDA-based quantitative proteomic strategies.