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Related Experiment Video

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Proteome-wide Quantification of Labeling Homogeneity at the Single Molecule Level
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SWATH enables precise label-free quantification on proteome scale.

Qiang Huang1, Lu Yang, Ji Luo

  • 1Interdisciplinary Research Center on Biology and Chemistry, Chinese Academy of Sciences, Shanghai, P. R. China; Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, P. R. China.

Proteomics
|January 7, 2015
PubMed
Summary
This summary is machine-generated.

Mass spectrometry-based proteomics using Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH) offers precise, label-free quantification of thousands of proteins from complex cell lysates, aiding biological discovery.

Keywords:
Label-freeMass spectrometrySWATHTechnology

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Area of Science:

  • Proteomics
  • Mass Spectrometry
  • Quantitative Biology

Background:

  • Mass spectrometry (MS)-based proteomics is vital for biological research.
  • Shotgun proteomics and quantitative proteomics (label-based and label-free) have limitations.
  • Sequential Window Acquisition of All Theoretical Mass Spectra (SWATH) is a novel data-independent acquisition technique.

Purpose of the Study:

  • To evaluate the proteome-wide quantification performance of the SWATH method.
  • To assess SWATH's accuracy and precision on complex mouse-cell lysate samples.
  • To determine SWATH's utility for large-scale label-free quantification.

Main Methods:

  • Proteome-wide analysis using SWATH data-independent acquisition.
  • Peptide spectral library matching for quantification.
  • Analysis of complex mouse-cell lysate samples without prefractionation.

Main Results:

  • Identification and quantification of 3600 proteins from mouse-cell lysate.
  • SWATH demonstrated outstanding quantification precision.
  • Quantification accuracy was reduced with large differences in protein abundance, but signal intensity remained linear with loading amounts.

Conclusions:

  • SWATH enables precise, label-free quantification at the proteome scale.
  • Despite minor accuracy limitations, SWATH is valuable for discovering biological correlates.
  • SWATH is a powerful tool for comprehensive proteomic analysis.