Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments

Nat Methods. 2013 Aug;10(8):768-73. doi: 10.1038/nmeth.2529. Epub 2013 Jun 30.


We report a technique to selectively and continuously label the proteomes of individual cell types in coculture, named cell type-specific labeling using amino acid precursors (CTAP). Through transgenic expression of exogenous amino acid biosynthesis enzymes, vertebrate cells overcome their dependence on supplemented essential amino acids and can be selectively labeled through metabolic incorporation of amino acids produced from heavy isotope-labeled precursors. When testing CTAP in several human and mouse cell lines, we could differentially label the proteomes of distinct cell populations in coculture and determine the relative expression of proteins by quantitative mass spectrometry. In addition, using CTAP we identified the cell of origin of extracellular proteins secreted from cells in coculture. We believe that this method, which allows linking of proteins to their cell source, will be useful in studies of cell-cell communication and potentially for discovery of biomarkers.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Animals
  • Base Sequence
  • Cell Line
  • Coculture Techniques / methods
  • Humans
  • Isotope Labeling / methods
  • Lysine / metabolism*
  • Mice
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis
  • Organisms, Genetically Modified
  • Proteome / biosynthesis*
  • Proteome / genetics
  • Proteomics / methods*
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics
  • Sequence Analysis, DNA
  • Tandem Mass Spectrometry


  • Proteome
  • RNA, Messenger
  • Lysine

Associated data

  • GENBANK/KC962560
  • GENBANK/KC962561
  • GENBANK/KC962562
  • GENBANK/KC962563
  • GEO/GSE43894
  • GEO/GSE43895