Article abstract

Nature Methods 5, 959 - 964 (2008)
Published online: 19 October 2008 | doi:10.1038/nmeth.1260

Decision tree–driven tandem mass spectrometry for shotgun proteomics

Danielle L Swaney1,3, Graeme C McAlister1,3 & Joshua J Coon1,2

Mass spectrometry has become a key technology for modern large-scale protein sequencing. Tandem mass spectrometry, the process of peptide ion dissociation followed by mass-to-charge ratio (m/z) analysis, is the critical component for peptide identification. Recent advances in mass spectrometry now permit two discrete, and complementary, types of peptide ion fragmentation: collision-activated dissociation (CAD) and electron transfer dissociation (ETD) on a single instrument. To exploit this complementarity and increase sequencing success rates, we designed and embedded a data-dependent decision tree algorithm (DT) to make unsupervised, real-time decisions of which fragmentation method to use based on precursor charge and m/z. Applying the DT to large-scale proteome analyses of Saccharomyces cerevisiae and human embryonic stem cells, we identified 53,055 peptides in total, which was greater than by using CAD (38,293) or ETD (39,507) alone. In addition, the DT method also identified 7,422 phosphopeptides, compared to either 2,801 (CAD) or 5,874 (ETD) phosphopeptides.

  1. Department of Chemistry, 1101 University Avenue, University of Wisconsin, Madison, Wisconsin 53706, USA.
  2. Department of Biomolecular Chemistry, 1300 University Avenue, University of Wisconsin, Madison, Wisconsin 53706, USA.
  3. These authors contributed equally to this work.

Correspondence to: Joshua J Coon1,2 e-mail:


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