A label-free quantification method by MS/MS TIC compared to SILAC and spectral counting in a proteomics screen Academic Article uri icon


MeSH Major

  • Proteomics
  • Tandem Mass Spectrometry


  • In order to assess the biological function of proteins and their modifications for understanding signaling mechanisms within cells as well as specific biomarkers to disease, it is important that quantitative information be obtained under different experimental conditions. Stable isotope labeling is a powerful method for accurately determining changes in the levels of proteins and PTMs; however, isotope labeling experiments suffer from limited dynamic range resulting in signal change ratios of less than approximately 20:1 using most commercial mass spectrometers. Label-free approaches to relative quantification in proteomics such as spectral counting have gained popularity since no additional chemistries are needed. Here, we show a label-free method for relative quantification based on the TIC from peptide MS/MS spectra collected from data-dependent runs can be used effectively as a quantitative measure and expands the dynamic range over isotope labeling experiments allowing for abundance differences up to approximately 60:1 in a screen for proteins that bind to phosphotyrosine residues.

publication date

  • March 2008



  • Academic Article



  • eng

Digital Object Identifier (DOI)

  • 10.1002/pmic.200700426

PubMed ID

  • 18324724

Additional Document Info

start page

  • 994

end page

  • 9


  • 8


  • 5