Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

Nat Methods. 2004 Oct;1(1):39-45. doi: 10.1038/nmeth705. Epub 2004 Sep 29.


To take advantage of the potential quantitative benefits offered by tandem mass spectrometry, we have modified the method in which tandem mass spectrum data are acquired in 'shotgun' proteomic analyses. The proposed method is not data dependent and is based on the sequential isolation and fragmentation of precursor windows (of 10 m/z) within the ion trap until a desired mass range has been covered. We compared the quantitative figures of merit for this method to those for existing strategies by performing an analysis of the soluble fraction of whole-cell lysates from yeast metabolically labeled in vivo with (15)N. To automate this analysis, we modified software (RelEx) previously written in the Yates lab to generate chromatograms directly from tandem mass spectra. These chromatograms showed improvements in signal-to-noise ratio of approximately three- to fivefold over corresponding chromatograms generated from mass spectrometry scans. In addition, to demonstrate the utility of the data-independent acquisition strategy coupled with chromatogram reconstruction from tandem mass spectra, we measured protein expression levels in two developmental stages of Caenorhabditis elegans.

Publication types

  • Evaluation Study
  • Research Support, U.S. Gov't, P.H.S.
  • Validation Study

MeSH terms

  • Algorithms*
  • Animals
  • Caenorhabditis elegans / physiology
  • Caenorhabditis elegans Proteins / analysis
  • Caenorhabditis elegans Proteins / metabolism*
  • Cells, Cultured
  • Chromatography / methods*
  • Complex Mixtures / analysis*
  • Gene Expression Regulation, Developmental / physiology
  • Peptides / analysis*
  • Peptides / chemistry
  • Peptides / metabolism
  • Proteomics / methods
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Sequence Analysis, Protein / methods*
  • Spectrometry, Mass, Electrospray Ionization / methods*


  • Caenorhabditis elegans Proteins
  • Complex Mixtures
  • Peptides