Genome-scale proteome quantification by DEEP SEQ mass spectrometry

Feng Zhou, Yu Lu, Scott B. Ficarro, Guillaume Adelmant, Wenyu Jiang, C. John Luckey and Jarrod A. Marto ()
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Feng Zhou: Dana-Farber Cancer Institute
Yu Lu: Dana-Farber Cancer Institute
Scott B. Ficarro: Dana-Farber Cancer Institute
Guillaume Adelmant: Dana-Farber Cancer Institute
Wenyu Jiang: Brigham and Women’s Hospital
C. John Luckey: Brigham and Women’s Hospital
Jarrod A. Marto: Dana-Farber Cancer Institute

Nature Communications, 2013, vol. 4, issue 1, 1-11

Abstract: Abstract 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.

Date: 2013
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DOI: 10.1038/ncomms3171

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