Advanced identification of proteins in uncharacterized proteomes by pulsed in vivo stable isotope labeling-based mass spectrometry

Mol Cell Proteomics. 2010 Jun;9(6):1157-66. doi: 10.1074/mcp.M900426-MCP200. Epub 2010 Feb 5.

Abstract

Despite progress in the characterization of their genomes, proteomes of several model organisms are often only poorly characterized. This problem is aggravated by the presence of large numbers of expressed sequence tag clones that lack homologues in other species, which makes it difficult to identify new proteins irrespective of whether such molecules are involved in species-specific biological processes. We have used a pulsed stable isotope labeling with amino acids in cell culture (SILAC)-based mass spectrometry method, which is based on the detection of paired peptides after [(13)C(6)]lysine incorporation into proteins in vivo, to greatly increase the confidence of protein identification in cross-species database searches. The method was applied to identify nearly 3000 proteins in regenerating tails of the urodele amphibian Notophthalmus viridescens, which possesses outstanding capabilities in the regeneration of complex tissues. We reason that pulsed in vivo SILAC represents a versatile tool to identify new proteins in species for which only limited sequence information exists.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amputation
  • Animals
  • Expressed Sequence Tags
  • Isotope Labeling / methods*
  • Lysine / metabolism
  • Mass Spectrometry / methods*
  • Molecular Sequence Data
  • Peptides / metabolism
  • Proteome / analysis*
  • Proteome / chemistry
  • Regeneration / physiology
  • Salamandridae / physiology
  • Sequence Homology, Nucleic Acid
  • Species Specificity
  • Tail / physiology

Substances

  • Peptides
  • Proteome
  • Lysine