{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002187","ANALYSIS_ID":"AN003581","VERSION":"1","CREATED_ON":"June 2, 2022, 3:13 pm"},

"PROJECT":{"PROJECT_TITLE":"Interplay of CodY and CcpA in regulating central metabolism and biofilm formation in S. aureus","PROJECT_TYPE":"Staphylococcus aureus","PROJECT_SUMMARY":"Staphylococcus aureus is a medically important pathogen that exhibit high metabolic versatility allowing it to infect various niches within a host. S. aureus utilizes two major transcriptional regulators, CodY and CcpA, to remodel metabolic and virulence gene expression in response to changing environmental conditions. Previous studies revealed that inactivation of either codY or ccpA has a pronounced impact on different aspects of staphylococcal physiology and pathogenesis. To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development we constructed and characterized codY ccpA double mutant in S. aureus UAMS-1. In line with previous studies, we found that CcpA and CodY control cellular metabolic status by altering carbon flow through the central and overflow metabolic pathways. Our results demonstrate that ccpA inactivation impairs biofilm formation and decreases incorporation of eDNA into the biofilm matrix while disrupting codY resulted in a robust structured biofilm tethered together with eDNA and PIA. Interestingly, inactivation of both codY and ccpA decreases biofilm biomass and neglects eDNA release in the double mutant. Compared to inactivation of codY, the codY ccpA mutant did not overexpress toxins but maintained overexpression of amino acid metabolism pathways. Furthermore, codY ccpA mutant produced higher amounts of PIA, in contrast to the wild-type strain and ccpA mutant. Overall, results of this study suggest that interplay between CodY and CcpA modulates central metabolism to optimize growth on preferred carbon sources while repressing virulence gene expression until nutrient limitation requires scavenging nutrients from the host","INSTITUTE":"University of Nebraska Medical Center","DEPARTMENT":"Pathology and Microbiology","LAST_NAME":"Sadykov","FIRST_NAME":"Marat","ADDRESS":"UNMC Department of Pathology and Microbiology 985900 Nebraska Medical Center Omaha, NE 68198-5900","EMAIL":"msadykov@unmc.edu","PHONE":"402-559-4186","CONTRIBUTORS":"Dhananjay Shinde, Ahn, Jongsom"},

"STUDY":{"STUDY_TITLE":"Interplay of CodY and CcpA in regulating central metabolism and biofilm formation in S. aureus","STUDY_TYPE":"Research","STUDY_SUMMARY":"Staphylococcus aureus is a medically important pathogen that exhibit high metabolic versatility allowing it to infect various niches within a host. S. aureus utilizes two major transcriptional regulators, CodY and CcpA, to remodel metabolic and virulence gene expression in response to changing environmental conditions. Previous studies revealed that inactivation of either codY or ccpA has a pronounced impact on different aspects of staphylococcal physiology and pathogenesis. To determine the contribution and interplay of these two regulators in modulating central metabolism, virulence, and biofilm development we constructed and characterized codY ccpA double mutant in S. aureus UAMS-1. In line with previous studies, we found that CcpA and CodY control cellular metabolic status by altering carbon flow through the central and overflow metabolic pathways. Our results demonstrate that ccpA inactivation impairs biofilm formation and decreases incorporation of eDNA into the biofilm matrix while disrupting codY resulted in a robust structured biofilm tethered together with eDNA and PIA. Interestingly, inactivation of both codY and ccpA decreases biofilm biomass and neglects eDNA release in the double mutant. Compared to inactivation of codY, the codY ccpA mutant did not overexpress toxins but maintained overexpression of amino acid metabolism pathways. Furthermore, codY ccpA mutant produced higher amounts of PIA, in contrast to the wild-type strain and ccpA mutant. Overall, results of this study suggest that interplay between CodY and CcpA modulates central metabolism to optimize growth on preferred carbon sources while repressing virulence gene expression until nutrient limitation requires scavenging nutrients from the host.","INSTITUTE":"University of Nebraska Medical Center","DEPARTMENT":"Pathology and Microbiology","LAST_NAME":"Sadykov","FIRST_NAME":"Marat","ADDRESS":"UNMC Department of Pathology and Microbiology 985900 Nebraska Medical Center Omaha, NE 68198-5900","EMAIL":"msadykov@unmc.edu","PHONE":"4025594186"},

"SUBJECT":{"SUBJECT_TYPE":"Bacteria","SUBJECT_SPECIES":"Staphylococcus aureus","TAXONOMY_ID":"1280","GENDER":"Not applicable"},
"SUBJECT_SAMPLE_FACTORS":[
{
"Subject ID":"-",
"Sample ID":"ccpA 6h_1",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"ccpA 6h_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"ccpA 6h_2",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"ccpA 6h_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"ccpA 6h_3",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"ccpA 6h_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"ccpA 3h_1",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"ccpA 3h_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"ccpA 3h_2",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"ccpA 3h_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"ccpA 3h_3",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"ccpA 3h_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY 6h_1",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"codY 6h_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY 6h_2",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"codY 6h_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY 6h_3",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"codY 6h_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY 3h_1",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"codY 3h_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY 3h_2",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"codY 3h_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY 3h_3",
"Factors":{"Genotype":"ccpA"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"codY 3h_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY ccpA 6h_1",
"Factors":{"Genotype":"codY ccpA"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"codY ccpA 6h_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY ccpA 6h_2",
"Factors":{"Genotype":"codY ccpA"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"codY ccpA 6h_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY ccpA 6h_3",
"Factors":{"Genotype":"codY ccpA"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"codY ccpA 6h_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY ccpA 3h_1",
"Factors":{"Genotype":"codY ccpA"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"codY ccpA 3h_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY ccpA 3h_2",
"Factors":{"Genotype":"codY ccpA"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"codY ccpA 3h_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"codY ccpA 3h_3",
"Factors":{"Genotype":"codY ccpA"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"codY ccpA 3h_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT 6h_1",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"WT 6h_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT 6h_2",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"WT 6h_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT 6h_3",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"Treatment":"6h","RAW_FILE_NAME":"WT 6h_3.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT 3h_1",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"WT 3h_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT 3h_2",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"WT 3h_2.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"WT 3h_3",
"Factors":{"Genotype":"WT"},
"Additional sample data":{"Treatment":"3h","RAW_FILE_NAME":"WT 3h_3.mzML"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Strains were inoculated in 3 ml of TSB containing 14 mM glucose in glass tubes (Fisher Scientific, cat# 14-961-29) for 16 h and adjusted to an OD600 of 0.05 in 50 ml TSB containing 14 mM glucose in 500 ml flasks and grown at 250 rpm, 37oC for 3 h or 6 h. Culture volumes corresponding to OD600 of 10 optical units were harvested and rapidly filtered through a membrane (0.45 μm, Millipore Cat# MIHAWG100) using Microfil® Filtration Funnels (Millipore, Cat# HAWG047S6) and EZ-FITTM Manifold Base, 6 Place Stainless Steel (Millipore, Cat# EZFITBASE6). The cells on the membrane were washed twice with 5 ml of 0.6% saline and then immediately quenched in 5 ml of ice-cold 60% ethanol containing Br-ATP (final concentration 2 μM) as internal control. The cells were mechanically disrupted using 0.1 mm diameter Glass beads (biospec, Cat# 11079101) and bead homogenizer for 30 s at 6,800 rpm, 3 cycles, 10 sec pause, 4oC(Precellys Evolution, bertin technologies) and centrifuged at 13,000 rpm, 10 min at 4oC to remove cell debris. The supernatant containing intracellular metabolites were separated, and 3 ml was added to 17 ml DW, frozen, lyophilized using FreeZone 4.5 Liter (labconco, Catalog #: 720401050), , and stored in a ultra-low temperature freezer set at -80°C until further analysis.","SAMPLE_TYPE":"Bacterial cells","STORAGE_CONDITIONS":"-20℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Staphylococcus aureus UAMS-1 wild-type strain (WT) Staphylococcus aureus UAMS-1 codY::ermC mutant (codY) Staphylococcus aureus UAMS-1 ccpA::tetM mutant (ccpA) Staphylococcus aureus UAMS-1 codY::ermC ccpA::tetM mutant (codY ccpA)"},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Strains were inoculated in 3 ml of TSB containing 14 mM glucose in glass tubes (Fisher Scientific, cat# 14-961-29) for 16 h and adjusted to an OD600 of 0.05 in 50 ml TSB containing 14 mM glucose in 500 ml flasks and grown at 250 rpm, 37oC for 3 h or 6 h. Culture volumes corresponding to OD600 of 10 optical units were harvested and rapidly filtered through a membrane (0.45 μm, Millipore Cat# MIHAWG100) using Microfil® Filtration Funnels (Millipore, Cat# HAWG047S6) and EZ-FITTM Manifold Base, 6 Place Stainless Steel (Millipore, Cat# EZFITBASE6). The cells on the membrane were washed twice with 5 ml of 0.6% saline and then immediately quenched in 5 ml of ice-cold 60% ethanol containing Br-ATP (final concentration 2 μM) as internal control. The cells were mechanically disrupted using 0.1 mm diameter Glass beads (biospec, Cat# 11079101) and bead homogenizer for 30 s at 6,800 rpm, 3 cycles, 10 sec pause, 4oC(Precellys Evolution, bertin technologies) and centrifuged at 13,000 rpm, 10 min at 4oC to remove cell debris. The supernatant containing intracellular metabolites were separated, and 3 ml was added to 17 ml DW, frozen, lyophilized using FreeZone 4.5 Liter (labconco, Catalog #: 720401050), , and stored in a ultra-low temperature freezer set at -80°C until further analysis.","PROCESSING_STORAGE_CONDITIONS":"On ice","EXTRACT_STORAGE":"-80℃"},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Triple-quadrupole-ion trap hybrid mass spectrometer viz., QTRAP6500+ (Sciex, USA) connected with ultra-performance liquid chromatography I-class (UPLC) system procured from Waters, USA was used for the metabolite analysis. The chromatographic separation was performed by liquid chromatography using XBridge Amide (150 × 2.1mm ID; 3.5µm particle size, Waters, USA) analytical column and a binary solvent system with a flow rate of 0.4 ml/min. A guard XBridge Amide column (20 × 2.1mm ID; 3.5µm particle size, Waters, USA) was connected in front of analytical column. Mobile phase A was composed of 10 mM ammonium acetate, 10mM ammonium hydroxide containing 5% acetonitrile in LC-MS grade water; mobile phase B was 100% LC-MS grade acetonitrile.","CHROMATOGRAPHY_TYPE":"HILIC","INSTRUMENT_NAME":"Waters Acquity I-Class","COLUMN_NAME":"Waters Acquity BEH Amide (150 x 2.1mm, 1.7um)"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS"},

"MS":{"INSTRUMENT_NAME":"ABI Sciex 6500+","INSTRUMENT_TYPE":"QTRAP","MS_TYPE":"ESI","ION_MODE":"UNSPECIFIED","MS_COMMENTS":"QTRAP6500+ operated in polarity switching mode was used for targeted quantitation of amino acids through Multiple Reaction Monitoring (MRM) process. Electrospray ionization (ESI) parameters were optimized are as follows: electrospray ion voltage of -4200V and 5500V in negative and positive mode respectively, source temperature of 400°C, curtain gas of 35, and gas 1 and 2 of 40 and 40 psi, respectively. Compound specific parameters were optimized for each compound using manual tuning. These parameters are declustering potential (DP) were 65V and -60V in positive and negative mode respectively, entrance potential (EP) was set at 10V and -10V in positive and negative mode respectively and collision cell exit potential (CXP) was maintained at 10V and -10V in positive and negative mode respectively. MRM data was analysed using Multiquant software."},

"MS_METABOLITE_DATA":{
"Units":"CPS",

"Data":[{"Metabolite":"Methylisocitrate","WT 3h_1":"1.30E+06","WT 3h_2":"2.30E+06","WT 3h_3":"2.30E+06","ccpA 3h_1":"2.70E+06","ccpA 3h_2":"2.80E+06","ccpA 3h_3":"2.70E+06","codY 3h_1":"2.40E+06","codY 3h_2":"2.20E+06","codY 3h_3":"9.50E+05","codY ccpA 3h_1":"2.20E+06","codY ccpA 3h_2":"1.30E+06","codY ccpA 3h_3":"2.10E+06","WT 6h_1":"2.00E+06","WT 6h_2":"2.10E+06","WT 6h_3":"2.20E+06","ccpA 6h_1":"2.60E+06","ccpA 6h_2":"2.30E+06","ccpA 6h_3":"2.20E+06","codY 6h_1":"2.10E+06","codY 6h_2":"2.10E+06","codY 6h_3":"1.90E+06","codY ccpA 6h_1":"2.10E+06","codY ccpA 6h_2":"2.00E+06","codY ccpA 6h_3":"2.30E+06"},{"Metabolite":"Cyclic GMP","WT 3h_1":"2.10E+04","WT 3h_2":"2.70E+04","WT 3h_3":"3.30E+04","ccpA 3h_1":"2.80E+04","ccpA 3h_2":"3.40E+04","ccpA 3h_3":"2.50E+04","codY 3h_1":"3.00E+04","codY 3h_2":"2.50E+04","codY 3h_3":"1.30E+04","codY ccpA 3h_1":"3.00E+04","codY ccpA 3h_2":"1.80E+04","codY ccpA 3h_3":"3.10E+04","WT 6h_1":"2.60E+04","WT 6h_2":"2.70E+04","WT 6h_3":"2.80E+04","ccpA 6h_1":"2.80E+04","ccpA 6h_2":"2.00E+04","ccpA 6h_3":"2.10E+04","codY 6h_1":"2.50E+04","codY 6h_2":"2.80E+04","codY 6h_3":"1.80E+04","codY ccpA 6h_1":"2.00E+04","codY ccpA 6h_2":"3.00E+04","codY ccpA 6h_3":"3.00E+04"},{"Metabolite":"AICAR","WT 3h_1":"1.70E+05","WT 3h_2":"1.60E+05","WT 3h_3":"7.30E+05","ccpA 3h_1":"5.60E+04","ccpA 3h_2":"6.70E+04","ccpA 3h_3":"6.80E+04","codY 3h_1":"1.10E+05","codY 3h_2":"8.90E+04","codY 3h_3":"1.10E+05","codY ccpA 3h_1":"5.40E+04","codY ccpA 3h_2":"6.50E+04","codY ccpA 3h_3":"5.10E+04","WT 6h_1":"1.80E+07","WT 6h_2":"1.90E+07","WT 6h_3":"1.40E+07","ccpA 6h_1":"3.40E+07","ccpA 6h_2":"1.90E+07","ccpA 6h_3":"3.50E+07","codY 6h_1":"5.20E+06","codY 6h_2":"4.40E+06","codY 6h_3":"5.10E+06","codY ccpA 6h_1":"4.70E+06","codY ccpA 6h_2":"5.30E+06","codY ccpA 6h_3":"4.00E+06"},{"Metabolite":"5-phosphoribosylamine","WT 3h_1":"2.50E+06","WT 3h_2":"2.90E+06","WT 3h_3":"2.30E+06","ccpA 3h_1":"2.40E+06","ccpA 3h_2":"2.40E+06","ccpA 3h_3":"2.40E+06","codY 3h_1":"2.40E+06","codY 3h_2":"2.40E+06","codY 3h_3":"2.30E+06","codY ccpA 3h_1":"2.40E+06","codY ccpA 3h_2":"2.20E+06","codY ccpA 3h_3":"2.30E+06","WT 6h_1":"2.40E+06","WT 6h_2":"2.50E+06","WT 6h_3":"2.30E+06","ccpA 6h_1":"2.20E+06","ccpA 6h_2":"2.40E+06","ccpA 6h_3":"2.20E+06","codY 6h_1":"2.10E+06","codY 6h_2":"2.30E+06","codY 6h_3":"2.20E+06","codY ccpA 6h_1":"2.70E+06","codY ccpA 6h_2":"2.70E+06","codY ccpA 6h_3":"2.70E+06"},{"Metabolite":"Acetyl CoA","WT 3h_1":"6.20E+06","WT 3h_2":"3.10E+06","WT 3h_3":"6.90E+06","ccpA 3h_1":"9.70E+05","ccpA 3h_2":"6.70E+06","ccpA 3h_3":"7.50E+06","codY 3h_1":"5.40E+06","codY 3h_2":"1.00E+07","codY 3h_3":"9.30E+06","codY ccpA 3h_1":"3.00E+06","codY ccpA 3h_2":"6.50E+06","codY ccpA 3h_3":"1.20E+07","WT 6h_1":"4.40E+05","WT 6h_2":"6.10E+05","WT 6h_3":"4.00E+05","ccpA 6h_1":"2.40E+05","ccpA 6h_2":"9.40E+05","ccpA 6h_3":"3.60E+05","codY 6h_1":"6.30E+05","codY 6h_2":"1.30E+06","codY 6h_3":"1.30E+06","codY ccpA 6h_1":"8.50E+05","codY ccpA 6h_2":"5.00E+05","codY ccpA 6h_3":"5.50E+06"},{"Metabolite":"Acetyl Dephospho CoA","WT 3h_1":"6.60E+05","WT 3h_2":"9.50E+05","WT 3h_3":"5.90E+05","ccpA 3h_1":"2.40E+05","ccpA 3h_2":"2.80E+05","ccpA 3h_3":"2.00E+05","codY 3h_1":"7.50E+05","codY 3h_2":"1.60E+05","codY 3h_3":"1.30E+05","codY ccpA 3h_1":"3.40E+05","codY ccpA 3h_2":"2.90E+05","codY ccpA 3h_3":"2.00E+05","WT 6h_1":"1.40E+05","WT 6h_2":"1.40E+05","WT 6h_3":"1.10E+05","ccpA 6h_1":"6.10E+04","ccpA 6h_2":"1.90E+05","ccpA 6h_3":"6.20E+04","codY 6h_1":"7.10E+04","codY 6h_2":"5.40E+04","codY 6h_3":"6.20E+04","codY ccpA 6h_1":"1.80E+05","codY ccpA 6h_2":"1.00E+05","codY ccpA 6h_3":"3.30E+05"},{"Metabolite":"Adenine","WT 3h_1":"5.60E+04","WT 3h_2":"1.00E+05","WT 3h_3":"1.50E+05","ccpA 3h_1":"4.10E+04","ccpA 3h_2":"1.00E+05","ccpA 3h_3":"9.80E+04","codY 3h_1":"6.70E+04","codY 3h_2":"7.60E+04","codY 3h_3":"7.30E+04","codY ccpA 3h_1":"7.90E+04","codY ccpA 3h_2":"1.20E+05","codY ccpA 3h_3":"8.10E+04","WT 6h_1":"1.70E+05","WT 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348.0"},{"Metabolite":"L-Alanine","HMDB":"HMDB0000161","Pubchem ID":"5950","KEGG ID":"C00041","MRM":"90.1 / 44.0"},{"Metabolite":"AMP","HMDB":"HMDB0000045","Pubchem ID":"6083","KEGG ID":"C00020","MRM":"346.0 / 79.0"},{"Metabolite":"L-Arginine","HMDB":"HMDB0000517","Pubchem ID":"6322","KEGG ID":"C00062","MRM":"175.2 / 70.0"},{"Metabolite":"L-Asparagine","HMDB":"HMDB0000168","Pubchem ID":"6267","KEGG ID":"C00152","MRM":"131.0 / 114.0"},{"Metabolite":"L-Aspartic acid","HMDB":"HMDB0000191","Pubchem ID":"5960","KEGG ID":"C00049","MRM":"132.0 / 88.0"},{"Metabolite":"ATP","HMDB":"HMDB0000538","Pubchem ID":"5957","KEGG ID":"C00002","MRM":"508.0 / 410.0"},{"Metabolite":"Cyclic AMP","HMDB":"HMDB0000058","Pubchem ID":"6076","KEGG ID":"C00575","MRM":"328.0 / 134.0"},{"Metabolite":"Citrulline","HMDB":"HMDB0000904","Pubchem ID":"9750","KEGG ID":"C00327","MRM":"174.0 / 131.0"},{"Metabolite":"Cytidine monophosphate","HMDB":"HMDB0000095","Pubchem ID":"8117","KEGG ID":"C00055","MRM":"324.0 / 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ID":"C00352","MRM":"258.0 / 97.0"},{"Metabolite":"D-Glucose 6-phosphate","HMDB":"HMDB0001401","Pubchem ID":"5958","KEGG ID":"C00092","MRM":"259.0 / 79.0"},{"Metabolite":"dGMP","HMDB":"HMDB0001044","Pubchem ID":"65059","KEGG ID":"C00362","MRM":"346.0 / 79.0"},{"Metabolite":"dGTP","HMDB":"HMDB0001440","Pubchem ID":"65103","KEGG ID":"C00286","MRM":"506.0 / 159.0"},{"Metabolite":"D-Ribulose 5-phosphate","HMDB":"HMDB0000618","Pubchem ID":"439184","KEGG ID":"C00199","MRM":"229.0 / 97.0"},{"Metabolite":"dTDP-D-glucose","HMDB":"HMDB0001328","Pubchem ID":"443210","KEGG ID":"C00842","MRM":"563.0 / 79.0"},{"Metabolite":"dTMP","HMDB":"HMDB0001227","Pubchem ID":"9700","KEGG ID":"C00364","MRM":"321.0 / 195.0"},{"Metabolite":"dTTP","HMDB":"HMDB0001342","Pubchem ID":"64968","KEGG ID":"C00459","MRM":"481.0 / 79.0"},{"Metabolite":"FAD","HMDB":"HMDB0001248","Pubchem ID":"643975","KEGG ID":"C00016","MRM":"784.0 / 79.0"},{"Metabolite":"CoA","HMDB":"HMDB0001423","Pubchem ID":"87642","KEGG ID":"C00010","MRM":"766.0 / 79.0"},{"Metabolite":"Fumarate","HMDB":"HMDB0000134","Pubchem ID":"444972","KEGG ID":"C00122","MRM":"115.0 / 71.0"},{"Metabolite":"D-Glucose","HMDB":"HMDB0000122","Pubchem ID":"5793","KEGG ID":"C00221","MRM":"179.1 / 89.1"},{"Metabolite":"Gluconate","HMDB":"HMDB0000625","Pubchem ID":"10690","KEGG ID":"C00257","MRM":"129.0 / 85.0"},{"Metabolite":"L-Glutamic acid","HMDB":"HMDB0000148","Pubchem ID":"33032","KEGG ID":"C00025","MRM":"148.1 / 84.0"},{"Metabolite":"L-Glutamine","HMDB":"HMDB0000641","Pubchem ID":"5961","KEGG ID":"C00064","MRM":"147.0 / 84.0"},{"Metabolite":"D-Glyceraldehyde 3-phosphate","HMDB":"HMDB0001112","Pubchem ID":"729","KEGG ID":"C00118","MRM":"169.0 / 79.0"},{"Metabolite":"Glycerol 3-phosphate","HMDB":"HMDB0000126","Pubchem ID":"439162","KEGG ID":"C00093","MRM":"171.0 / 63.0"},{"Metabolite":"Glycine","HMDB":"HMDB0000123","Pubchem ID":"750","KEGG ID":"C00037","MRM":"76.0 / 30.0"},{"Metabolite":"GMP","HMDB":"HMDB0001397","Pubchem ID":"6804","KEGG ID":"C00144","MRM":"362.0 / 79.0"},{"Metabolite":"Guanosine","HMDB":"HMDB0000133","Pubchem ID":"6802","KEGG ID":"C00387","MRM":"282.0 / 133.0"},{"Metabolite":"D-Galactose","HMDB":"HMDB0000143","Pubchem ID":"439357","KEGG ID":"C00984","MRM":"179.0 / 89.0"},{"Metabolite":"IMP","HMDB":"HMDB0000175","Pubchem ID":"8582","KEGG ID":"C00130","MRM":"349.0 / 137.0"},{"Metabolite":"Inosine","HMDB":"HMDB0000195","Pubchem ID":"6021","KEGG ID":"C00294","MRM":"269.0 / 137.0"},{"Metabolite":"ITP","HMDB":"HMDB0000189","Pubchem ID":"8583","KEGG ID":"C00081","MRM":"507.0 / 409.0"},{"Metabolite":"L-Leucine","HMDB":"HMDB0000687","Pubchem ID":"6106","KEGG ID":"C00123","MRM":"132.1 / 86.0"},{"Metabolite":"L-Lysine","HMDB":"HMDB0000182","Pubchem ID":"5962","KEGG ID":"C00047","MRM":"147.1 / 84.0"},{"Metabolite":"L-Malic acid","HMDB":"HMDB0000156","Pubchem ID":"222656","KEGG ID":"C00149","MRM":"133.0 / 115.0"},{"Metabolite":"L-Methionine","HMDB":"HMDB0000696","Pubchem ID":"6137","KEGG ID":"C00073","MRM":"150.2 / 104.0"},{"Metabolite":"NADP","HMDB":"HMDB0000217","Pubchem ID":"5886","KEGG ID":"C00006","MRM":"744.0 / 604.0"},{"Metabolite":"NAD","HMDB":"HMDB0000902","Pubchem ID":"5893","KEGG ID":"C00003","MRM":"662.0 / 540.0"},{"Metabolite":"NADH","HMDB":"HMDB0001487","Pubchem ID":"928","KEGG ID":"C00004","MRM":"664.0 / 408.0"},{"Metabolite":"Nicotinamide riboside","HMDB":"HMDB0000855","Pubchem ID":"439924","KEGG ID":"C03150","MRM":"335.0 / 123.0"},{"Metabolite":"Ornithine","HMDB":"HMDB0000214","Pubchem ID":"6262","KEGG ID":"C00077","MRM":"133.1 / 70.1"},{"Metabolite":"Oxaloacetate","HMDB":"HMDB0000223","Pubchem ID":"970","KEGG ID":"C00036","MRM":"131.0 / 87.0"},{"Metabolite":"Oxidized glutathione","HMDB":"HMDB0003337","Pubchem ID":"975","KEGG ID":"C00127","MRM":"611.0 / 272.0"},{"Metabolite":"L-Phenylalanine","HMDB":"HMDB0000159","Pubchem ID":"6140","KEGG ID":"C00079","MRM":"166.1 / 120.1"},{"Metabolite":"Phosphoenolpyruvate","HMDB":"HMDB0000263","Pubchem ID":"1005","KEGG ID":"C00074","MRM":"167.0 / 79.0"},{"Metabolite":"Citrate","HMDB":"HMDB0000094","Pubchem ID":"311","KEGG ID":"C00158","MRM":"191.0 / 111.0"},{"Metabolite":"L-Proline","HMDB":"HMDB0000162","Pubchem ID":"145742","KEGG ID":"C00148","MRM":"116.1 / 70.0"},{"Metabolite":"Pyridoxal phosphate","HMDB":"HMDB0001491","Pubchem ID":"1051","KEGG ID":"C00018","MRM":"248.1 / 150.1"},{"Metabolite":"Pyruvate","HMDB":"HMDB0000243","Pubchem ID":"1060","KEGG ID":"C00022","MRM":"87.0 / 32.0"},{"Metabolite":"D-Sedoheptulose 7-phosphate","HMDB":"HMDB0001068","Pubchem ID":"22833559","KEGG ID":"C05382","MRM":"289.0 / 79.0"},{"Metabolite":"L-Serine","HMDB":"HMDB0000187","Pubchem ID":"5951","KEGG ID":"C00065","MRM":"106.1 / 60.0"},{"Metabolite":"L-Theanine","HMDB":"HMDB0034365","Pubchem ID":"439378","KEGG ID":"C01047","MRM":"175.0 / 84.0"},{"Metabolite":"Thiamine","HMDB":"HMDB0000235","Pubchem ID":"1130","KEGG ID":"C00378","MRM":"265.2 / 247.0"},{"Metabolite":"Thiamine pyrophosphate","HMDB":"HMDB0001372","Pubchem ID":"1132","KEGG ID":"C00068","MRM":"425.4 / 304.3"},{"Metabolite":"L-Threonine","HMDB":"HMDB0000167","Pubchem ID":"6288","KEGG ID":"C00188","MRM":"120.1 / 103.2"},{"Metabolite":"Thymine","HMDB":"HMDB0000262","Pubchem ID":"1135","KEGG ID":"C00178","MRM":"125.0 / 42.0"},{"Metabolite":"L-Tryptophan","HMDB":"HMDB0000929","Pubchem ID":"6305","KEGG ID":"C00078","MRM":"205.1 / 146.0"},{"Metabolite":"L-Tyrosine","HMDB":"HMDB0000158","Pubchem ID":"6057","KEGG ID":"C00082","MRM":"182.1 / 165.2"},{"Metabolite":"Uridine 5'-diphosphate","HMDB":"HMDB0000295","Pubchem ID":"6031","KEGG ID":"C00015","MRM":"403.0 / 159.0"},{"Metabolite":"Uridine diphosphate glucose","HMDB":"HMDB0000286","Pubchem ID":"53477679","KEGG ID":"C00029","MRM":"565.0 / 323.0"},{"Metabolite":"Uridine 5'-monophosphate","HMDB":"HMDB0000288","Pubchem ID":"6030","KEGG ID":"C00105","MRM":"323.0 / 97.0"},{"Metabolite":"Uracil","HMDB":"HMDB0000300","Pubchem ID":"1174","KEGG ID":"C00106","MRM":"111.0 / 42.0"},{"Metabolite":"Uridine","HMDB":"HMDB0000296","Pubchem ID":"6029","KEGG ID":"C00299","MRM":"245.0 / 113.0"},{"Metabolite":"Uridine triphosphate","HMDB":"HMDB0000285","Pubchem ID":"6133","KEGG ID":"C00075","MRM":"483.0 / 79.0"},{"Metabolite":"L-Valine","HMDB":"HMDB0000883","Pubchem ID":"6287","KEGG ID":"C00183","MRM":"118.0 / 72.0"},{"Metabolite":"Xanthine","HMDB":"HMDB0000292","Pubchem ID":"1188","KEGG ID":"C00385","MRM":"151.0 / 108.0"},{"Metabolite":"2-Oxoglutarate","HMDB":"HMDB0000208","Pubchem ID":"51","KEGG ID":"C00026","MRM":"145.0 / 101.0"},{"Metabolite":"6-Phospho-D-gluconate","HMDB":"HMDB0001316","Pubchem ID":"91493","KEGG ID":"C00345","MRM":"275.0 / 97.0"},{"Metabolite":"Acetyl phosphate","HMDB":"HMDB0001494","Pubchem ID":"186","KEGG ID":"C00227","MRM":"139.0 / 63.0"},{"Metabolite":"Adenosine","HMDB":"HMDB0000050","Pubchem ID":"60961","KEGG ID":"C00212","MRM":"266.0 / 134.0"},{"Metabolite":"ADP-glucose","HMDB":"HMDB0006557","Pubchem ID":"16500","KEGG ID":"C00498","MRM":"588.0 / 79.0"},{"Metabolite":"alpha-D-Ribose 5-phosphate","HMDB":"HMDB0001548","Pubchem ID":"440101","KEGG ID":"C03736","MRM":"229.0 / 97.0"},{"Metabolite":"Biotin","HMDB":"HMDB0000030","Pubchem ID":"171548","KEGG ID":"C00120","MRM":"243.0 / 42.0"},{"Metabolite":"cis-Aconitate","HMDB":"HMDB0000072","Pubchem ID":"643757","KEGG ID":"C00417","MRM":"173.0 / 129.0"},{"Metabolite":"CoASH","HMDB":"HMDB0001423","Pubchem ID":"87642","KEGG ID":"C00010","MRM":"766.0 / 79.0"},{"Metabolite":"dADP","HMDB":"HMDB0001508","Pubchem ID":"53477733","KEGG ID":"C00206","MRM":"410.0 / 159.0"},{"Metabolite":"D-Arabinose 5-phosphate","HMDB":"HMDB0011734","Pubchem ID":"188324","KEGG ID":"C01112","MRM":"229.0 / 97.0"},{"Metabolite":"dCDP","HMDB":"HMDB0001245","Pubchem ID":"150855","KEGG ID":"C00705","MRM":"386.0 / 159.0"},{"Metabolite":"D-Glucose 1-phosphate","HMDB":"HMDB0001586","Pubchem ID":"3403","KEGG ID":"C00103","MRM":"259.0 / 241.0"},{"Metabolite":"Dihydroxyacetone phosphate","HMDB":"HMDB0001473","Pubchem ID":"668","KEGG ID":"C00111","MRM":"169.0 / 97.0"},{"Metabolite":"dIMP","HMDB":"HMDB0006555","Pubchem ID":"91531","KEGG ID":"C06196","MRM":"331.0 / 79.0"},{"Metabolite":"Folate","HMDB":"HMDB0000121","Pubchem ID":"6037","KEGG ID":"C00504","MRM":"440.0 / 311.0"},{"Metabolite":"GDP","HMDB":"HMDB0001201","Pubchem ID":"8977","KEGG ID":"C00035","MRM":"442.0 / 79.0"},{"Metabolite":"L-Histidine","HMDB":"HMDB0000177","Pubchem ID":"6274","KEGG ID":"C00135","MRM":"156.1 / 110.0"},{"Metabolite":"Hypoxanthine","HMDB":"HMDB0000157","Pubchem ID":"790","KEGG ID":"C00262","MRM":"135.0 / 92.0"},{"Metabolite":"Lactate","HMDB":"HMDB0000190","Pubchem ID":"61503","KEGG ID":"C00186","MRM":"89.0 / 45.0"},{"Metabolite":"Malonyl-CoA","HMDB":"HMDB0001175","Pubchem ID":"10663","KEGG ID":"C03188","MRM":"852.0 / 79.0"},{"Metabolite":"Methylmalonate","HMDB":"HMDB0000202","Pubchem ID":"487","KEGG ID":"C02170","MRM":"117.0 / 73.0"},{"Metabolite":"NAAD","HMDB":"HMDB0001179","Pubchem ID":"583440","KEGG ID":"C00857","MRM":"665.0 / 428.1"},{"Metabolite":"NADPH","HMDB":"HMDB0000221","Pubchem ID":"22833512","KEGG ID":"C00005","MRM":"744.0 / 408.0"},{"Metabolite":"Oxalate","HMDB":"HMDB0002329","Pubchem ID":"971","KEGG ID":"C00209","MRM":"89.0 / 45.0"},{"Metabolite":"Phenylpyruvate","HMDB":"HMDB0000205","Pubchem ID":"997","KEGG ID":"C00166","MRM":"163.0 / 91.0"},{"Metabolite":"Shikimate","HMDB":"HMDB0003070","Pubchem ID":"8742","KEGG ID":"C00493","MRM":"173.0 / 73.0"},{"Metabolite":"Succinate","HMDB":"HMDB0000254","Pubchem ID":"1110","KEGG ID":"C00042","MRM":"117.0 / 99.0"},{"Metabolite":"Succinyl CoA","HMDB":"HMDB0001022","Pubchem ID":"439161","KEGG ID":"C00091","MRM":"866.0 / 79.0"},{"Metabolite":"Urate","HMDB":"HMDB0000289","Pubchem ID":"1175","KEGG ID":"C00366","MRM":"167.0 / 124.0"}]
}

}