Quantitative analysis of complex peptide mixtures using FTMS and differential mass spectrometry

J Am Soc Mass Spectrom. 2007 Feb;18(2):226-33. doi: 10.1016/j.jasms.2006.09.014. Epub 2006 Oct 25.


Label-free LC-MS profiling is a powerful quantitative proteomic method to study relative peptide abundances between two or more biological samples. Here we demonstrate the use of a previously described comparative LC-MS method, differential mass spectrometry (dMS), to analyze high-resolution Fourier transform mass spectrometry (FTMS) data for detection and quantification of known peptide differences between two sets of complex mixtures. Six standard peptides were spiked into a processed plasma background at fixed ratios from 1.25:1 to 4:1 to make two sets of samples. The resulting mixtures were analyzed by microcapillary LC-FTMS and dMS. dMS successfully identified five out of the six peptides as statistically significant differences (p <or= 0.005). In this experiment, the smallest fold change reliably detected by our method was 1.5:1, and the errors of estimated ratios of concentrations were less than 20% for peptides spiked at 1.5:1 to 4:1. We conclude that LC-FTMS coupled with dMS is a useful label-free quantitative MS method that can be used to detect subtle yet statistically significant peptide differences in complex protein mixtures, including plasma samples.

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cattle
  • Chromatography, High Pressure Liquid
  • Complex Mixtures / chemistry*
  • Humans
  • Molecular Sequence Data
  • Peptide Mapping
  • Peptides / chemistry*
  • Proteins / chemistry*
  • Rats
  • Reproducibility of Results
  • Spectroscopy, Fourier Transform Infrared*


  • Complex Mixtures
  • Peptides
  • Proteins