Cell-free synthesis of stable isotope-labeled internal standards for targeted quantitative proteomics

Schrödinger, 1945 Karr, 2012, A whole-cell computational model predicts phenotype from genotype, Cell, 150, 389, 10.1016/j.cell.2012.05.044 Matsuura, 2017, Reaction dynamics analysis of a reconstituted Escherichia coli protein translation system by computational modeling, Proc Natl Acad Sci U S A, 114, E1336, 10.1073/pnas.1615351114 Cox, 2011, Quantitative, high-resolution proteomics for data-driven systems biology, Annu Rev Biochem, 80, 273, 10.1146/annurev-biochem-061308-093216 Sato, 2006, Feedback repression is required for mammalian circadian clock function, Nat Genet, 38, 312, 10.1038/ng1745 Taniguchi, 2010, Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells, Science, 329, 533, 10.1126/science.1188308 Saito, 2012, Luminescent proteins for high-speed single-cell and whole-body imaging, Nat Commun, 3, 1262, 10.1038/ncomms2248 de Godoy, 2008, Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast, Nature, 455, 1251, 10.1038/nature07341 Nagaraj, 2011, Deep proteome and transcriptome mapping of a human cancer cell line, Mol Syst Biol, 7, 548, 10.1038/msb.2011.81 Beck, 2011, The quantitative proteome of a human cell line, Mol Syst Biol, 7, 549, 10.1038/msb.2011.82 Kim, 2014, A draft map of the human proteome, Nature, 509, 575, 10.1038/nature13302 Wilhelm, 2014, Mass-spectrometry-based draft of the human proteome, Nature, 509, 582, 10.1038/nature13319 Deshmukh, 2015, Deep proteomics of mouse skeletal muscle enables quantitation of protein isoforms, metabolic pathways, and transcription factors, Mol Cell Proteomics, 14, 841, 10.1074/mcp.M114.044222 Keshishian, 2007, Quantitative, multiplexed assays for low abundance proteins in plasma by targeted mass spectrometry and stable isotope dilution, Mol Cell Proteomics, 6, 2212, 10.1074/mcp.M700354-MCP200 Di Palma, 2012, ZIC-cHILIC as a fractionation method for sensitive and powerful shotgun proteomics, Nat Protoc, 7, 2041, 10.1038/nprot.2012.124 Brun, 2009, Isotope dilution strategies for absolute quantitative proteomics, J Proteomics, 72, 740, 10.1016/j.jprot.2009.03.007 Desiderio, 1983, Preparation of stable isotope-incorporated peptide internal standards for field desorption mass spectrometry quantification of peptides in biologic tissue, Biomed Mass Spectrom, 10, 471, 10.1002/bms.1200100806 Gerber, 2003, Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS, Proc Natl Acad Sci U S A, 100, 6940, 10.1073/pnas.0832254100 Merrifield, 1963, Solid phase peptide synthesis. I. The synthesis of a tetrapeptide, J Am Chem Soc, 85, 2149, 10.1021/ja00897a025 Hilpert, 2007, Peptide arrays on cellulose support: SPOT synthesis, a time and cost efficient method for synthesis of large numbers of peptides in a parallel and addressable fashion, Nat Protoc, 2, 1333, 10.1038/nprot.2007.160 Picotti, 2010, High-throughput generation of selected reaction-monitoring assays for proteins and proteomes, Nat Methods, 7, 43, 10.1038/nmeth.1408 Hsu, 2003, Stable-isotope dimethyl labeling for quantitative proteomics, Anal Chem, 75, 6843, 10.1021/ac0348625 Boersema, 2009, Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics, Nat Protoc, 4, 484, 10.1038/nprot.2009.21 Tsujino, 2013, Establishment of TSH β real-time monitoring system in mammalian photoperiodism, Genes Cells, 18, 575, 10.1111/gtc.12063 Ode, 2017, Knockout-rescue embryonic stem cell-derived mouse reveals circadian-period control by quality and quantity of CRY1, Mol Cell, 65, 176, 10.1016/j.molcel.2016.11.022 Ong, 2002, Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics, Mol Cell Proteomics, 1, 376, 10.1074/mcp.M200025-MCP200 Kruger, 2008, SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function, Cell, 134, 353, 10.1016/j.cell.2008.05.033 Gouw, 2010, Quantitative proteomics by metabolic labeling of model organisms, Mol Cell Proteomics, 9, 11, 10.1074/mcp.R900001-MCP200 Geiger, 2010, Super-SILAC mix for quantitative proteomics of human tumor tissue, Nat Methods, 7, 383, 10.1038/nmeth.1446 Larance, 2011, Stable-isotope labeling with amino acids in nematodes, Nat Methods, 8, 849, 10.1038/nmeth.1679 Geiger, 2013, Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse, Mol Cell Proteomics, 12, 1709, 10.1074/mcp.M112.024919 Hanke, 2008, Absolute SILAC for accurate quantitation of proteins in complex mixtures down to the attomole level, J Proteome Res, 7, 1118, 10.1021/pr7007175 Beynon, 2005, Multiplexed absolute quantification in proteomics using artificial QCAT proteins of concatenated signature peptides, Nat Methods, 2, 587, 10.1038/nmeth774 Brownridge, 2012, Absolute multiplexed protein quantification using QconCAT technology, Methods Mol Biol, 893, 267, 10.1007/978-1-61779-885-6_18 Shimizu, 2006, Cell-free translation systems for protein engineering, FEBS J, 273, 4133, 10.1111/j.1742-4658.2006.05431.x Harris, 2012, Cell-free biology: exploiting the interface between synthetic biology and synthetic chemistry, Curr Opin Biotechnol, 23, 672, 10.1016/j.copbio.2012.02.002 Rosenblum, 2014, Engine out of the chassis: cell-free protein synthesis and its uses, FEBS Lett, 588, 261, 10.1016/j.febslet.2013.10.016 Zemella, 2015, Cell-free protein synthesis: pros and cons of prokaryotic and eukaryotic systems, Chembiochem, 16, 2420, 10.1002/cbic.201500340 Nirenberg, 1961, The dependence of cell-free protein synthesis in E. coli upon naturally occurring or synthetic polyribonucleotides, Proc Natl Acad Sci U S A, 47, 1588, 10.1073/pnas.47.10.1588 Foster, 2014, In memoriam: geoffrey Louis Zubay, 1931-2014. Pioneer in cell-free gene expression studies and molecular genetics, Trends Biochem Sci, 39, 505, 10.1016/j.tibs.2014.07.007 Pratt, 2006, Multiplexed absolute quantification for proteomics using concatenated signature peptides encoded by QconCAT genes, Nat Protoc, 1, 1029, 10.1038/nprot.2006.129 Mirzaei, 2008, Comparative evaluation of current peptide production platforms used in absolute quantification in proteomics, Mol Cell Proteomics, 7, 813, 10.1074/mcp.M700495-MCP200 Brun, 2007, Isotope-labeled protein standards: toward absolute quantitative proteomics, Mol Cell Proteomics, 6, 2139, 10.1074/mcp.M700163-MCP200 Dupuis, 2008, Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks, Proteomics, 8, 4633, 10.1002/pmic.200800326 Janecki, 2007, A multiple reaction monitoring method for absolute quantification of the human liver alcohol dehydrogenase ADH1C1 isoenzyme, Anal Biochem, 369, 18, 10.1016/j.ab.2007.06.043 Ozawa, 2004, Optimization of an Escherichia coli system for cell-free synthesis of selectively N-labelled proteins for rapid analysis by NMR spectroscopy, Eur J Biochem, 271, 4084, 10.1111/j.1432-1033.2004.04346.x Yokoyama, 2011, A practical method for cell-free protein synthesis to avoid stable isotope scrambling and dilution, Anal Biochem, 411, 223, 10.1016/j.ab.2011.01.017 Stergachis, 2011, Rapid empirical discovery of optimal peptides for targeted proteomics, Nat Methods, 8, 1041, 10.1038/nmeth.1770 Simicevic, 2013, Absolute quantification of transcription factors during cellular differentiation using multiplexed targeted proteomics, Nat Methods, 10, 570, 10.1038/nmeth.2441 Horvatovich, 2015, In vitro transcription/translation system: a versatile tool in the search for missing proteins, J Proteome Res, 14, 3441, 10.1021/acs.jproteome.5b00486 Madin, 2000, A highly efficient and robust cell-free protein synthesis system prepared from wheat embryos: plants apparently contain a suicide system directed at ribosomes, Proc Natl Acad Sci U S A, 97, 559, 10.1073/pnas.97.2.559 Sawasaki, 2002, A cell-free protein synthesis system for high-throughput proteomics, Proc Natl Acad Sci U S A, 99, 14652, 10.1073/pnas.232580399 Singh, 2009, FLEXIQuant: a novel tool for the absolute quantification of proteins, and the simultaneous identification and quantification of potentially modified peptides, J Proteome Res, 8, 2201, 10.1021/pr800654s Singh, 2012, FLEXIQinase, a mass spectrometry-based assay, to unveil multikinase mechanisms, Nat Methods, 9, 504, 10.1038/nmeth.1970 Takemori, 2015, High-throughput synthesis of stable isotope-labeled transmembrane proteins for targeted transmembrane proteomics using a wheat germ cell-free protein synthesis system, Mol Biosyst, 11, 361, 10.1039/C4MB00556B Takemori, 2016, High-throughput production of a stable isotope-labeled peptide library for targeted proteomics using a wheat germ cell-free synthesis system, Mol Biosyst, 12, 2389, 10.1039/C6MB00209A DeSouza, 2008, Multiple reaction monitoring of mTRAQ-labeled peptides enables absolute quantification of endogenous levels of a potential cancer marker in cancerous and normal endometrial tissues, J Proteome Res, 7, 3525, 10.1021/pr800312m Ross, 2004, Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents, Mol Cell Proteomics, 3, 1154, 10.1074/mcp.M400129-MCP200 Matsumoto, 2017, A large-scale targeted proteomics assay resource based on an in vitro human proteome, Nat Methods, 14, 251, 10.1038/nmeth.4116 Shimizu, 2001, Cell-free translation reconstituted with purified components, Nat Biotechnol, 19, 751, 10.1038/90802 Ohashi, 2007, Efficient protein selection based on ribosome display system with purified components, Biochem Biophys Res Commun, 352, 270, 10.1016/j.bbrc.2006.11.017 Shimizu, 2010, PURE technology, Methods Mol Biol, 607, 11, 10.1007/978-1-60327-331-2_2 Shimizu, 2014, The PURE system for protein production, Methods Mol Biol, 1118, 275, 10.1007/978-1-62703-782-2_19 Wang, 2012, Multiplexed in vivo His-tagging of enzyme pathways for in vitro single-pot multienzyme catalysis, ACS Synth Biol, 1, 43, 10.1021/sb3000029 Li, 2014, Improved cell-free RNA and protein synthesis system, PLoS One, 9, e106232, 10.1371/journal.pone.0106232 Shepherd, 2017, De novo design and synthesis of a 30-cistron translation-factor module, Nucleic Acids Res, 45, 10895, 10.1093/nar/gkx753 Villarreal, 2018, Synthetic microbial consortia enable rapid assembly of pure translation machinery, Nat Chem Biol, 14, 29, 10.1038/nchembio.2514 Xian, 2016, Peptide biosynthesis with stable isotope labeling from a cell-free expression system for targeted proteomics with absolute quantification, Mol Cell Proteomics, 15, 2819, 10.1074/mcp.O115.056507 Narumi, 2016, Mass spectrometry-based absolute quantification reveals rhythmic variation of mouse circadian clock proteins, Proc Natl Acad Sci U S A, 113, E3461, 10.1073/pnas.1603799113 Ahn, 2005, Cell-free synthesis of recombinant proteins from PCR-amplified genes at a comparable productivity to that of plasmid-based reactions, Biochem Biophys Res Commun, 338, 1346, 10.1016/j.bbrc.2005.10.094 Jun, 2008, Continuous-exchange cell-free protein synthesis using PCR-generated DNA and an RNase E-deficient extract, Biotechniques, 44, 387, 10.2144/000112690 Katsura, 2017, A reproducible and scalable procedure for preparing bacterial extracts for cell-free protein synthesis, J Biochem, 162, 357, 10.1093/jb/mvx039 Jiang, 1998, Escherichia coli prlC gene encodes a trypsin-like proteinase regulating the cell cycle, J Biochem, 124, 980, 10.1093/oxfordjournals.jbchem.a022216 Lawless, 2016, Direct and absolute quantification of over 1800 yeast proteins via selected reaction monitoring, Mol Cell Proteomics, 15, 1309, 10.1074/mcp.M115.054288 Glatter, 2012, Large-scale quantitative assessment of different in-solution protein digestion protocols reveals superior cleavage efficiency of tandem Lys-C/trypsin proteolysis over trypsin digestion, J Proteome Res, 11, 5145, 10.1021/pr300273g Tsiatsiani, 2015, Proteomics beyond trypsin, FEBS J, 282, 2612, 10.1111/febs.13287 Giansanti, 2016, Six alternative proteases for mass spectrometry-based proteomics beyond trypsin, Nat Protoc, 11, 993, 10.1038/nprot.2016.057 Ufarté, 2015, Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology, Front Microbiol, 6, 563 DeCastro, 2016, Metagenomics of thermophiles with a focus on discovery of novel thermozymes, Front Microbiol, 7, 1521, 10.3389/fmicb.2016.01521 Huang, 2016, The coming of age of de novo protein design, Nature, 537, 320, 10.1038/nature19946