{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002890","ANALYSIS_ID":"AN004748","VERSION":"1","CREATED_ON":"September 29, 2023, 6:40 pm"},

"PROJECT":{"PROJECT_TITLE":"Characterization of the in vivo deuteration of native phospholipids by mass spectrometry yields guidelines for their regiospecific customization","PROJECT_SUMMARY":"Customization of deuterated biomolecules is vital for many advanced biological experiments, including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating E. coli lipids in vivo, this approach has not been widely implemented. Here, an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of thirty-six lipid species were quantitatively profiled in fifteen different growth conditions and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.","INSTITUTE":"University of Tennessee","DEPARTMENT":"Genome Science and Technology (Bredesen Center)","LAST_NAME":"Matthew","FIRST_NAME":"Keller","ADDRESS":"The Bredesen Center for Interdisciplinary Research and Graduate Education 444 Greve Hall, 821 Volunteer Blvd","EMAIL":"qrh579@vols.utk.edu","PHONE":"18659747999","PUBLICATIONS":"In review at Analytical Chemistry","CONTRIBUTORS":"Qiu Zhang, Shuo Qian, Brian Sanders, Hugh O''Neill, Robert Hettich"},

"STUDY":{"STUDY_TITLE":"Characterization of the in vivo deuteration of native phospholipids by mass spectrometry yields guidelines for their regiospecific customization","STUDY_SUMMARY":"Customization of deuterated biomolecules is vital for many advanced biological experiments, including neutron scattering. However, because it is challenging to control the proportion and regiospecificity of deuterium incorporation in live systems, often only two or three synthetic lipids are mixed together to form simplistic model membranes. This limits the applicability and biological accuracy of the results generated with these synthetic membranes. Despite some limited prior examination of deuterating E. coli lipids in vivo, this approach has not been widely implemented. Here, an extensive mass spectrometry-based profiling of E. coli phospholipid deuteration states with several different growth media was performed and a computational method to describe deuterium distributions with a one-number summary is introduced. The deuteration states of thirty-six lipid species were quantitatively profiled in fifteen different growth conditions and tandem mass spectrometry was used to reveal deuterium localization. Regressions were employed to enable the prediction of lipid deuteration for untested conditions. Small-angle neutron scattering was performed on select deuterated lipid samples, which validated the deuteration states calculated from the mass spectral data. Based on these experiments, guidelines for the design of specifically deuterated phospholipids are described. This unlocks even greater capabilities from neutron-based techniques, enabling experiments that were formerly impossible.","INSTITUTE":"University of Tennessee","DEPARTMENT":"Genome Science and Technology (Bredesen Center)","LAST_NAME":"Matthew","FIRST_NAME":"Keller","ADDRESS":"The Bredesen Center for Interdisciplinary Research and Graduate Education 444 Greve Hall, 821 Volunteer Blvd. Knoxville, TN 37996-3394","EMAIL":"qrh579@vols.utk.edu","PHONE":"18659747999"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Escherichia coli","GENOTYPE_STRAIN":"BL21(DE3)"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"50D-Gly/0_1-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_0_1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/0_2-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_0_2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/0_3-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_0_3-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/100_1-neg",
"Factors":{"Carbon source":"D-Glucose","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_100_1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/100_2-neg",
"Factors":{"Carbon source":"D-Glucose","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_100_2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/100_3-neg",
"Factors":{"Carbon source":"D-Glucose","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_100_3-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Glu/0_1-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"25","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Glu_0_1_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Glu/0_2-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"25","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Glu_0_2_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Glu/0_3-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"25","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Glu_0_3_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Glu/100-neg_tech-rep1",
"Factors":{"Carbon source":"D-Glucose","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Glu_100_tech1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Glu/100-neg_tech-rep2",
"Factors":{"Carbon source":"D-Glucose","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"2","RAW_FILE_NAME":"D-Glu_100_tech2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/0_1-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"50","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_0_1_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/0_2-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"50","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_0_2_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/0_3-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"50","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_0_3_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/100_1-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"75","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_100_1_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/100_2-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"75","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_100_2_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/100_3-neg",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"75","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_100_3_neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/100-neg_tech-rep1",
"Factors":{"Carbon source":"D-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_100_tech1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/100-neg_tech-rep2",
"Factors":{"Carbon source":"D-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"2","RAW_FILE_NAME":"H-Glu_100_tech2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/25_1-neg",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_25_1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/25_2-neg",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_25_2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/25_3-neg",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_25_3-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/50_1-neg",
"Factors":{"Carbon source":"D-Glycerol","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_50_1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/50_2-neg",
"Factors":{"Carbon source":"D-Glycerol","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_50_2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/50_3-neg",
"Factors":{"Carbon source":"D-Glycerol","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_50_3-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/75_1-neg",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_75_1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/75_2-neg",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_75_2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/75_3-neg",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_75_3-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/75_repeat_1-neg",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_75_1-neg_2ndbatch.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/75_repeat_2-neg",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_75_2-neg_2ndbatch.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/75_repeat_3-neg",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_75_3-neg_2ndbatch.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/0-neg_tech-rep1",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_0_tech1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/0-neg_tech-rep2",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"0","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"2","RAW_FILE_NAME":"H-Gly_0_tech2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/100_1-neg",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_100_1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/100_2-neg",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_100_2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/100_3-neg",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"100","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_100_3-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/25-neg_tech-rep1",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"25","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_25_tech1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/25-neg_tech-rep2",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"25","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"2","RAW_FILE_NAME":"H-Gly_25_tech2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/50-neg_tech-rep1",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"50","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_50_tech1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/50-neg_tech-rep2",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"50","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"2","RAW_FILE_NAME":"H-Gly_50_tech2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/75-neg_tech-rep1",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"75","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_75_tech1-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/75-neg_tech-rep2",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"75","MS ionization mode":"negative"},
"Additional sample data":{"Technical replicate":"2","RAW_FILE_NAME":"H-Gly_75_tech2-neg.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/0_1-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_0_1-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/0_2-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_0_2-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/0_3-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_0_3-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/100_1-pos",
"Factors":{"Carbon source":"D-Glucose","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_100_1-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/100_2-pos",
"Factors":{"Carbon source":"D-Glucose","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_100_2-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"50D-Gly/100_3-pos",
"Factors":{"Carbon source":"D-Glucose","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"50D-Gly_100_3-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Glu/0_1-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"25","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Glu_0_1_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Glu/0_2-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"25","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Glu_0_2_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Glu/0_3-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"25","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Glu_0_3_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Glu/100-pos",
"Factors":{"Carbon source":"D-Glucose","Percent D2O":"0","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Glu_100_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/0_1-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"50","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_0_1_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/0_2-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"50","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_0_2_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/0_3-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"50","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_0_3_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/100_1-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"75","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_100_1_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/100_2-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"75","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_100_2_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"D-Gly/100_3-pos",
"Factors":{"Carbon source":"H-Glucose","Percent D2O":"75","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"D-Gly_100_3_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/100-pos",
"Factors":{"Carbon source":"D-Glycerol","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_100_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/25_1-pos",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"0","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_25_1-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/25_2-pos",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"0","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_25_2-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/25_3-pos",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"0","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_25_3-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/50_1-pos",
"Factors":{"Carbon source":"D-Glycerol","Percent D2O":"0","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_50_1-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/50_2-pos",
"Factors":{"Carbon source":"D-Glycerol","Percent D2O":"0","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_50_2-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/50_3-pos",
"Factors":{"Carbon source":"D-Glycerol","Percent D2O":"0","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_50_3-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/75_1-pos",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_75_1-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/75_2-pos",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_75_2-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Glu/75_3-pos",
"Factors":{"Carbon source":"50/50 H/D-Glycerol","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Glu_75_3-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/0-pos",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"0","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_0_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/100_1-pos",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_100_1-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/100_2-pos",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_100_2-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/100_3-pos",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"100","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_100_3-pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/25-pos",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"25","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_25_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/50-pos",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"50","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_50_pos.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"H-Gly/75-pos",
"Factors":{"Carbon source":"H-Glycerol","Percent D2O":"75","MS ionization mode":"positive"},
"Additional sample data":{"Technical replicate":"1","RAW_FILE_NAME":"H-Gly_75_pos.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Lipids were extracted from E coli cell pellets following the Matyash protocol with slight variations described in the manuscript supplemental. Cell lysis was performed with bead beating or ultrasonication. Extraction solvents were in the ratio 10:3:25 MTBE:methanol:water. See publication for more detail.","COLLECTION_PROTOCOL_FILENAME":"Deuterated_Lipids_Methods_Summary.pdf","SAMPLE_TYPE":"Bacterial cells"},

"TREATMENT":{"TREATMENT_SUMMARY":"E. coli was grown in Enfors minimal media (deuterated or otherwise) with different carbon sources including glycerol, glucose, D-glycerol, and D-glucose.","CELL_MEDIA":"Enfors minimal media","CELL_HARVESTING":"30 mL culture collected by centrifugation at 4k x g"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Lipids were extracted from E coli cell pellets following the Matyash protocol with slight variations described in the manuscript supplemental. Cell lysis was performed with bead beating or ultrasonication. Extraction solvents were in the ratio 10:3:25 MTBE:methanol:water. See publication for more detail.","SAMPLEPREP_PROTOCOL_FILENAME":"Deuterated_Lipids_Methods_Summary.pdf","EXTRACTION_METHOD":"Matyash (MTBE) varient","SAMPLE_RESUSPENSION":"8:23:69 butanol:isopropanol:water"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Because the columns were packed in-house, there is some variation in the total length (see column description below).","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Dionex Ultimate 3000 RS","COLUMN_NAME":"In-house packed nano column (ID 100 μm, Kinetex 1.7 μm C18 (100 Å) [Phenomenex], 12-15 cm.","SOLVENT_A":"60% acetonitrile/40% water; ~0.4g/L ammonium acetate","SOLVENT_B":"90% sopropanol/10% acetonitrile; ~0.4g/L ammonium acetate","FLOW_GRADIENT":"Solvent Gradient: Time (min) 0 1 2.5 7.5 13.5 48.5 58.5 75.5 77.5 87 Solvent A (%) 99 99 70 65 45 30 1 1 99 99 Solvent B (%) 1 1 30 45 55 70 99 99 1 1","FLOW_RATE":"Split flow nano-chromatography. The actual flow rate at the column is dependent on a variety of factors and an accurate measurement of the flow rate is impractical. The flow rate at the macro pumps were set at either 0.05 or 0.1 mL/min depending on the waste line''s backpressure.","COLUMN_TEMPERATURE":"room temp","METHODS_FILENAME":"Deuterated_Lipids_Methods_Summary.pdf"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","ANALYSIS_PROTOCOL_FILE":"Deuterated_Lipids_Methods_Summary.pdf"},

"MS":{"INSTRUMENT_NAME":"Thermo Velos Pro Orbitrap","INSTRUMENT_TYPE":"LTQ-FT","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Top 10 DDA acquisition: Oribitrap Full-Scan at 30k resolving power from 150-2000 m/z. Data-dependent collisional-induced dissociation (CID) fragmentation scans performed with the LTQ ion trap at 30 normalized collision energy with normal scan rate."},

"MS_METABOLITE_DATA":{
"Units":"Presence/Absence",

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}

}