Targeted mass spectrometric analysis of N-terminally truncated isoforms generated via alternative translation initiation

FEBS Lett. 2009 Jul 21;583(14):2441-5. doi: 10.1016/j.febslet.2009.05.042. Epub 2009 May 28.


Alternative translation initiation is a mechanism whereby functionally altered proteins are produced from a single mRNA. Internal initiation of translation generates N-terminally truncated protein isoforms, but such isoforms observed in immunoblot analysis are often overlooked or dismissed as degradation products. We identified an N-terminally truncated isoform of human Dok-1 with N-terminal acetylation as seen in the wild-type. This Dok-1 isoform exhibited distinct perinuclear localization whereas the wild-type protein was distributed throughout the cytoplasm. Targeted analysis of blocked N-terminal peptides provides rapid identification of protein isoforms and could be widely applied for the general evaluation of perplexing immunoblot bands.

MeSH terms

  • Alternative Splicing*
  • Amino Acid Sequence
  • Cell Line
  • DNA-Binding Proteins* / chemistry
  • DNA-Binding Proteins* / genetics
  • DNA-Binding Proteins* / metabolism
  • Humans
  • Molecular Sequence Data
  • Peptide Chain Initiation, Translational*
  • Phosphoproteins* / chemistry
  • Phosphoproteins* / genetics
  • Phosphoproteins* / metabolism
  • Protein Biosynthesis
  • Protein Isoforms* / chemistry
  • Protein Isoforms* / genetics
  • Protein Isoforms* / metabolism
  • Protein Processing, Post-Translational
  • RNA-Binding Proteins* / chemistry
  • RNA-Binding Proteins* / genetics
  • RNA-Binding Proteins* / metabolism
  • Sequence Alignment


  • DNA-Binding Proteins
  • DOK1 protein, human
  • Phosphoproteins
  • Protein Isoforms
  • RNA-Binding Proteins