title: Genome-scale proteome quantification by DEEP SEQ mass spectrometry.
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.
authors.affiliation: Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215-5450, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Zhou
authors.forename: Yu
authors.initials: Y
authors.lastname: Lu
authors.forename: Scott B
authors.initials: SB
authors.lastname: Ficarro
authors.forename: Guillaume
authors.initials: G
authors.lastname: Adelmant
authors.forename: Wenyu
authors.initials: W
authors.lastname: Jiang
authors.forename: C John
authors.initials: CJ
authors.lastname: Luckey
authors.forename: Jarrod A
authors.initials: JA
authors.lastname: Marto
mesh_terms: D000818:Animals; D002454:Cell Differentiation; D002853:Chromatography, Liquid / Q000379:methods; D053595:Embryonic Stem Cells / Q000166:cytology / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D005855:Germ Layers / Q000166:cytology / Q000378:metabolism*; D051379:Mice; D010446:Peptide Fragments / Q000032:analysis*; D014176:Protein Biosynthesis; D020543:Proteome / Q000235:genetics* / Q000378:metabolism; D020539:Sequence Analysis, Protein / Q000379:methods*; D053719:Tandem Mass Spectrometry / Q000379:methods; D014357:Trypsin / Q000737:chemistry
chemical_list: D010446:Peptide Fragments; D020543:Proteome; D014357:Trypsin