DataEntryID 123
    General information
      Manuscript title: Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast.
      PubMed ID: http://www.ncbi.nlm.nih.gov/pubmed/28365149
      Journal: Cell Systems
      Year: 2017
      Authors: Petri-Jaan Lahtvee, Benjamín J. Sánchez, Agata Smialowska, Sergo Kasvandik, Ibrahim E. Elsemman, Francesco Gatto, Jens Nielsen
      Affiliations: Department of Biology and Biological Engineering, Systems and Synthetic Biology, Chalmers University of Technology, Kemivägen 10, 412 96 Gothenburg, Sweden.
      Keywords: integrative data analysis, absolute proteome, absolute transcriptome, protein turnover, protein degradation rates, translation efficiency, genome-scale metabolic modeling, translational control
      Full text article: https://www.kimosys.org/rails/active_storage/blobs/eyJfcmFpbHMiOnsibWVzc2FnZSI6IkJBaHBBdXNFIiwiZXhwIjpudWxsLCJwdXIiOiJibG9iX2lkIn19--d5d27a8355577841e66769aba0f1a3276fd86911/Lahtvee_2017.pdf
      Project name: not specified

    Experiment description
      Organism: Saccharomyces cerevisiae
      Strain: CEN.PK113-7D ΔLYS1
      Data type: enzyme/protein concentrations
      Data units: pgDW
      Execution date: not specified

    Experimental details
      Temperature (°C): 30
      pH: 5.5
      Carbon source: glucose
      Culture mode: chemostat
      Process condition: aerobic
      Dilution rate (h⁻¹): 0.1
      Working volume: 1 L
      Biomass concentration (g/L): see original paper
      Medium composition: Base medium used contained 10 g glucose, 5 g (NH4)2SO4, 3 g KH2PO4 and 0.5 g MgSO4 per litre, in addition to 1 mL of trace elements solution and 1 mL of vitamin solution. The trace element solution contained, per litre (pH=4): EDTA (sodium salt), 15.0 g; ZnSO4⋅7H2O, 4.5 g; MnCl2⋅2H2O, 0.84 g; CoCl2⋅6H2O, 0.3 g; CuSO4⋅5H2O, 0.3 g; Na2MoO4⋅2H2O, 0.4 g; CaCl2⋅2H2O, 4.5 g; FeSO4⋅7H2O, 3.0 g; H3BO3, 1.0 g; and KI, 0.10 g.). The vitamin solution contained, per liter (pH=6.5): biotin, 0.05 g; p-amino benzoic acid, 0.2 g; nicotinic acid, 1 g; Ca-pantothenate, 1 g; pyridoxine-HCl, 1 g; thiamine-HCl, 1 g and myo-inositol, 25 g.
      General protocol information: Measurement method: LC-MS/MS;
      Methods description: Quantitative Proteome Measurements: The peak intensity-based absolute quantification method iBAQ was chosen for protein quantification [1]. First, a lysine auxotrophic strain was created by deleting the LYS1 gene. Latter strain was cultivated with a labelled heavy 15N, 13C-lysine (Cambridge Isotope Laboratories), and fully labelled biomass was produced (in which 98% of proteogenic lysine was labelled, data not shown) and used as an internal standard in the measurements.                                                                                                                  
Nano-LC/MS/MS Analysis: Injected peptides (2 μg) were separated on an Ultimate 3000 RSLCnano system (Dionex, Sunnyvale, California, United States) using a C18 cartridge trap-column in a backflush configuration and an in-house packed (3 μm C18 particles, Dr Maisch) analytical 50 cm x 75 μm emitter-column (New Objective). The peptides were eluted at 200 nL min−1 with an 8%–40% B 240 min gradient (buffer B: 80% acetonitrile + 0.1% formic acid, buffer A: 0.1% formic acid) to a Q Exactive (Thermo Fisher Scientific) tandem mass spectrometer operating with a top-10 strategy and a cycle time of 0.9 seconds. Briefly, one 350-1 400 m/z MS scan at a resolution of R = 70,000 was followed by higher-energy collisional dissociation fragmentation (normalized collision energy of 25) of the 10 most-intense ions (charge states +2 to +6) at R = 17,500. The MS and MS/MS ion target values were 3x 106 and 5x 104, respectively. Dynamic exclusion was limited to 80 seconds.
------------------------------------References----------------------------------
[1] Schwanhäusser B., Busse D., Li N., Dittmar G., Schuchhardt J., Wolf J., Chen W., Selbach M.Nature. 2011; 473: 337-342. http://doi.org/bgjkh9
      Data file: http://kimosys.org/repository/123/download?parameter=1258; 
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    Submission and curation
      Entered by: Administrator KiMoSys
      Created: 2018-09-20 17:22:27 UTC
      Updated: 2020-04-24 16:10:37 UTC
      Version: 0
      Status: (reviewed) 2018-09-20 17:22:32 UTC
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