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Related Concept Videos

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Tandem mass spectrometry, also known as MS/MS or MS2, is an analytical technique that employs two mass analyzers. Essentially it is a series of mass spectrometers that helps isolate a particular biomolecule and then helps study its chemical properties.
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Updated: Feb 23, 2026

Deep Proteome Profiling by Isobaric Labeling, Extensive Liquid Chromatography, Mass Spectrometry, and Software-assisted Quantification
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MdFDIA: A Mass Defect Based Four-Plex Data-Independent Acquisition Strategy for Proteome Quantification.

Yi Di, Ying Zhang, Lei Zhang

  • 1Department of Chemistry, Fudan University , Shanghai, 200433, People's Republic of China.

Analytical Chemistry
|September 6, 2017
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Summary

A new mass defect-based four-plex data-independent acquisition (MdFDIA) strategy enables parallel proteome quantification. This method combines stable isotope labeling with amino acids in cell culture (SILAC) and dimethyl labeling for enhanced accuracy in complex biological samples.

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Area of Science:

  • Proteomics
  • Quantitative Mass Spectrometry
  • Biotechnology

Background:

  • Data-independent acquisition (DIA) offers sensitive and reproducible proteome quantification.
  • A limitation of DIA is the lack of compatible multiplexed quantification methods.
  • Existing methods often require additional complexity in tandem mass spectrometry (MS2) spectra analysis.

Purpose of the Study:

  • To develop a novel multiplexed quantification strategy for DIA.
  • To enhance the accuracy and reduce the impact of chromatographic isotope effects in DIA.
  • To enable parallel analysis of four protein samples in a single DIA experiment.

Main Methods:

  • Developed a mass defect-based four-plex data-independent acquisition (MdFDIA) strategy.
  • Combined stable isotope labeling with amino acids in cell culture (SILAC) using 13C615N2-lysine and D8-lysine.
  • Utilized in vitro dimethyl labeling with light and heavy dimethyl groups on digested peptides.
  • Analyzed the four pseudoisobaric labeled samples using DIA on an Orbitrap Fusion Lumos instrument.

Main Results:

  • MdFDIA successfully quantified four multiplexed proteome samples without MS2 spectra complexity.
  • Demonstrated a significant reduction in the adverse impact of chromatographic isotope effects, particularly the deuterium effect.
  • Provided a method for validating fragment types in DIA spectra identification.
  • Successfully applied MdFDIA to quantitative proteome analysis of four breast cancer cell lines.

Conclusions:

  • MdFDIA is a feasible and robust strategy for parallel quantitative proteome analysis.
  • This method overcomes a key bottleneck in DIA by enabling efficient multiplexing.
  • MdFDIA enhances quantitative accuracy and has broad applicability in biological research.