A combination of neutral loss and targeted product ion scanning with two enzymatic digestions facilitates the comprehensive mapping of phosphorylation sites

Proteomics. 2007 Aug;7(15):2522-9. doi: 10.1002/pmic.200700026.


We propose here a new strategy for the exhaustive mapping of phosphorylation sites in the Xenopus laevis Cdc25 phosphatase, which regulates cell cycle progression in eukaryotic cells. Two different MS analyses in a linear IT were used to identify the phosphorylated residues. First, a data-dependent neutral loss (DDNL) analysis triggered the fragmentation of peptides that show enhanced neutral loss of phosphoric acid. Second, a targeted product ion scanning (TPIS) mass analysis was carried out in which MS2 events are triggered for specific m/z values. Full coverage of the protein sequence was obtained by combining the two analyses with two enzymatic digestions, trypsin and chymotrypsin, yielding a comprehensive map of the phosphorylation sites. Previous reports have shown Cdc25C to be phosphorylated by Cdc2-cyclin B at four residues (Thr48, Thr67, Thr138 and Ser205). By using this combination of scan modes, we have identified four additional phosphorylation sites (Thr86, Ser99, Thr112 and Ser163) in a recombinant Cdc25C protein containing 198 residues of the NH2-terminal noncatalytic domain. The sensitivity of this combined approach makes it extremely useful for the comprehensive characterization of phosphorylation sites, virtually permitting complete coverage of the protein sequence with peptides within the mass detection range of the linear IT.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Animals
  • Cell Cycle Proteins / chemistry
  • Cell Cycle Proteins / genetics
  • Cell Cycle Proteins / metabolism*
  • Chymotrypsin / pharmacology*
  • Escherichia coli / genetics
  • Glutathione Transferase / metabolism
  • Mass Spectrometry / methods*
  • Molecular Sequence Data
  • Peptide Mapping / methods*
  • Phosphorylation
  • Protein Structure, Tertiary
  • Recombinant Proteins / chemistry
  • Recombinant Proteins / metabolism
  • Sensitivity and Specificity
  • Spectrometry, Mass, Electrospray Ionization
  • Trypsin / pharmacology*
  • Xenopus
  • cdc25 Phosphatases / chemistry
  • cdc25 Phosphatases / genetics
  • cdc25 Phosphatases / metabolism*


  • Cell Cycle Proteins
  • Recombinant Proteins
  • Glutathione Transferase
  • cdc25 Phosphatases
  • Chymotrypsin
  • Trypsin