Genome-scale proteome quantification by DEEP SEQ mass spectrometry Academic Article uri icon

  • Overview
  • Research
  • Identity
  • Additional Document Info
  • View All


  • Advances in chemistry and massively parallel detection underlie DNA-sequencing platforms that are poised for application in personalized medicine. In stark contrast, systematic generation of protein-level data lags well behind genomics in virtually every aspect: depth of coverage, throughput, ease of sample preparation and experimental time. Here, to bridge this gap, we develop an approach based on simple detergent lysis and single-enzyme digest, extreme, orthogonal separation of peptides and true nanoflow liquid chromatography-tandem mass spectrometry that provides high peak capacity and ionization efficiency. This automated, deep efficient peptide sequencing and quantification mass spectrometry platform provides genome-scale proteome coverage equivalent to RNA-seq ribosomal profiling and accurate quantification for multiplexed isotope labels. In a model of the embryonic to epiblast transition in murine stem cells, we unambiguously quantify 11,352 gene products that span 70% of Swiss-Prot and capture protein regulation across the full detectable range of high-throughput gene expression and protein translation.


  • Zhou, Feng
  • Lu, Yu
  • Ficarro, Scott B
  • Adelmant, Guillaume
  • Jiang, Wenyu
  • Luckey, C John
  • Marto, Jarrod A

publication date

  • October 2013