Decision Tree-Driven Tandem Mass Spectrometry for Shotgun Proteomics

By D. Swaney, G. McAlister, Joshua J. Coon. Nature Methods, 2008

311 citations recorded by the source corpus.

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.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/18e5c56eba7470ddea9268bd35176beecd2e986a

Citations in the corpus

• Universal database search tool for proteomics (2014, unknown): “…trypsin, LysC, ArgC, GluC or AspN, separated into 12 fractions via strong cation exchange chromatography and analysed in triplicate with an ETD-enabled LTQ-Orbitrap mass spectrometer, where peptide fragmentation was accomplished either with CID or ETD using the decision-tree acquisition mode 54 .”