Zhou, FengLu, YuFicarro, ScottAdelmant, GuillaumeJiang, WenyuLuckey, C. JohnMarto, Jarrod2014-03-112013Zhou, Feng, Yu Lu, Scott B. Ficarro, Guillaume Adelmant, Wenyu Jiang, C. John Luckey, and Jarrod A. Marto. 2013. “Genome-scale Proteome Quantification by DEEP SEQ Mass Spectrometry.” Nature communications 4 (1): 2171. doi:10.1038/ncomms3171. http://dx.doi.org/10.1038/ncomms3171.2041-1723http://nrs.harvard.edu/urn-3:HUL.InstRepos:11879679Advances 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 LC-MS/MS that provides high peak capacity and ionization efficiency. This automated, deep efficient peptide sequencing and quantification (DEEP SEQ) 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.en-USQuantitative proteomicsmass spectrometryLC-MSMS/MSgene expressionmicroarrayprotein translationribosomal profilingpluripotencyembryonic stem cellsJournal Article2014-03-1110.1038/ncomms3171