Phosphoproteome analysis of Drosophila melanogaster embryos

J Proteome Res. 2008 Apr;7(4):1675-82. doi: 10.1021/pr700696a. Epub 2008 Mar 8.


Protein phosphorylation is a key regulatory event in most cellular processes and development. Mass spectrometry-based proteomics provides a framework for the large-scale identification and characterization of phosphorylation sites. Here, we used a well-established phosphopeptide enrichment and identification strategy including the combination of strong cation exchange chromatography, immobilized metal affinity chromatography, and high-accuracy mass spectrometry instrumentation to study phosphorylation in developing Drosophila embryos. In total, 13,720 different phosphorylation sites were discovered from 2702 proteins with an estimated false-discovery rate (FDR) of 0.63% at the peptide level. Because of the large size of the data set, both novel and known phosphorylation motifs were extracted using the Motif-X algorithm, including those representative of potential ordered phosphorylation events.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Animals
  • Chromatography, Affinity / methods
  • Chromatography, Ion Exchange / methods
  • Drosophila Proteins / analysis*
  • Drosophila Proteins / metabolism
  • Drosophila melanogaster / embryology
  • Drosophila melanogaster / metabolism*
  • Embryo, Nonmammalian / metabolism*
  • Models, Biological
  • Phosphoproteins / analysis*
  • Phosphoproteins / metabolism
  • Phosphorylation
  • Proteomics / methods*
  • Signal Transduction / physiology
  • Tandem Mass Spectrometry / methods
  • Trypsin / metabolism


  • Drosophila Proteins
  • Phosphoproteins
  • Trypsin