#METABOLOMICS WORKBENCH lgafeira_20230913_021756 DATATRACK_ID:4312 STUDY_ID:ST002868 ANALYSIS_ID:AN004701 PROJECT_ID:PR001791 VERSION 1 CREATED_ON September 13, 2023, 3:02 am #PROJECT PR:PROJECT_TITLE Pathogenic Staphylococcus epidermidis ICE25 response to skin and blood pH PR:PROJECT_TYPE Proteomic and metabolomic study PR:PROJECT_SUMMARY Staphylococcus epidermidis (SE) is one of the most common bacteria of the human PR:PROJECT_SUMMARY skin microbiota. Despite its role as a commensal, SE has emerged as an PR:PROJECT_SUMMARY opportunistic pathogen, associated with 80% of medical devices related PR:PROJECT_SUMMARY infections. Moreover, these bacteria are extremely difficult to treat due to PR:PROJECT_SUMMARY their ability to form biofilms and accumulate resistance to almost all classes PR:PROJECT_SUMMARY of antimicrobials developed so far. Thus new preventive and therapeutic PR:PROJECT_SUMMARY strategies are urgently needed. In spite of its clinical importance, the PR:PROJECT_SUMMARY molecular mechanisms associated with SE colonisation and disease are still PR:PROJECT_SUMMARY poorly understood. A deeper understanding of the metabolic and cellular PR:PROJECT_SUMMARY processes associated with response to environmental factors characteristic of SE PR:PROJECT_SUMMARY ecological niches in health and disease might provide new clues on colonisation PR:PROJECT_SUMMARY and disease processes. Here we studied the impact of pH conditions, mimicking PR:PROJECT_SUMMARY the skin pH (5.5) and blood pH (7.4), in a S. epidermidis pathogenic strain, PR:PROJECT_SUMMARY belonging to the A/C clonal lineage, by means of next-generation proteomics and PR:PROJECT_SUMMARY 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes PR:PROJECT_SUMMARY occurring when a sudden pH change arise, simulating the skin barrier break PR:PROJECT_SUMMARY produced by a catheter. PR:INSTITUTE ITQB NOVA PR:LAST_NAME Gonçalves PR:FIRST_NAME Luís PR:ADDRESS Avenida Republica, Oeiras, Not USCanada, 2780-157 Oeiras, Portugal PR:EMAIL lgafeira@itqb.unl.pt PR:PHONE 214469464 #STUDY ST:STUDY_TITLE Pathogenic Staphylococcus epidermidis ICE25 response to skin and blood pH ST:STUDY_SUMMARY Staphylococcus epidermidis (SE) is one of the most common bacteria of the human ST:STUDY_SUMMARY skin microbiota. Despite its role as a commensal, SE has emerged as an ST:STUDY_SUMMARY opportunistic pathogen, associated with 80% of medical devices related ST:STUDY_SUMMARY infections. Moreover, these bacteria are extremely difficult to treat due to ST:STUDY_SUMMARY their ability to form biofilms and accumulate resistance to almost all classes ST:STUDY_SUMMARY of antimicrobials developed so far. Thus new preventive and therapeutic ST:STUDY_SUMMARY strategies are urgently needed. In spite of its clinical importance, the ST:STUDY_SUMMARY molecular mechanisms associated with SE colonisation and disease are still ST:STUDY_SUMMARY poorly understood. A deeper understanding of the metabolic and cellular ST:STUDY_SUMMARY processes associated with response to environmental factors characteristic of SE ST:STUDY_SUMMARY ecological niches in health and disease might provide new clues on colonisation ST:STUDY_SUMMARY and disease processes. Here we studied the impact of pH conditions, mimicking ST:STUDY_SUMMARY the skin pH (5.5) and blood pH (7.4), in a S. epidermidis pathogenic strain, ST:STUDY_SUMMARY belonging to the A/C clonal lineage, by means of next-generation proteomics and ST:STUDY_SUMMARY 1H NMR-based metabolomics. Moreover, we evaluated the metabolic changes ST:STUDY_SUMMARY occurring when a sudden pH change arise, simulating the skin barrier break ST:STUDY_SUMMARY produced by a catheter. ST:INSTITUTE ITQB NOVA ST:LAST_NAME Gonçalves ST:FIRST_NAME Luís G. ST:ADDRESS Avenida Republica ST:EMAIL lgafeira@itqb.unl.pt ST:PHONE 214469464 #SUBJECT SU:SUBJECT_TYPE Bacteria SU:SUBJECT_SPECIES Staphylococcus epidermidis SU:TAXONOMY_ID 1282 SU:GENOTYPE_STRAIN Staphylococcus epidermidis ICE25 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - SE_1_190530 Class:I77 RAW_FILE_NAME=SE_1_190530 SUBJECT_SAMPLE_FACTORS - SE_10_190530 Class:I57 RAW_FILE_NAME=SE_10_190530 SUBJECT_SAMPLE_FACTORS - SE_11_190530 Class:I57 RAW_FILE_NAME=SE_11_190530 SUBJECT_SAMPLE_FACTORS - SE_18_190530 Class:I55 RAW_FILE_NAME=SE_18_190530 SUBJECT_SAMPLE_FACTORS - SE_23_190530 Class:I55 RAW_FILE_NAME=SE_23_190530 SUBJECT_SAMPLE_FACTORS - SE_24_190530 Class:I55 RAW_FILE_NAME=SE_24_190530 SUBJECT_SAMPLE_FACTORS - SE_4_190530 Class:I57 RAW_FILE_NAME=SE_4_190530 SUBJECT_SAMPLE_FACTORS - SE_5_190530 Class:I77 RAW_FILE_NAME=SE_5_190530 SUBJECT_SAMPLE_FACTORS - SE_6_190530 Class:I77 RAW_FILE_NAME=SE_6_190530 SUBJECT_SAMPLE_FACTORS - SE_7_190530 Class:I57 RAW_FILE_NAME=SE_7_190530 SUBJECT_SAMPLE_FACTORS - SE_9_190530 Class:I77 RAW_FILE_NAME=SE_9_190530 SUBJECT_SAMPLE_FACTORS - SE_a03_190712 Class:I57 RAW_FILE_NAME=SE_a03_190712 SUBJECT_SAMPLE_FACTORS - SE_a04_190712 Class:I55 RAW_FILE_NAME=SE_a04_190712 SUBJECT_SAMPLE_FACTORS - SE_a06_190712 Class:I77 RAW_FILE_NAME=SE_a06_190712 SUBJECT_SAMPLE_FACTORS - SE_a07_190712 Class:I55 RAW_FILE_NAME=SE_a07_190712 SUBJECT_SAMPLE_FACTORS - SE_a09_190712 Class:I57 RAW_FILE_NAME=SE_a09_190712 SUBJECT_SAMPLE_FACTORS - SE_a11_190712 Class:I55 RAW_FILE_NAME=SE_a11_190712 SUBJECT_SAMPLE_FACTORS - SE_a12_190712 Class:I77 RAW_FILE_NAME=SE_a12_190712 SUBJECT_SAMPLE_FACTORS - SE_a13_190712_rep Class:I57 RAW_FILE_NAME=SE_a13_190712_rep SUBJECT_SAMPLE_FACTORS - SE_a16_190712 Class:I77 RAW_FILE_NAME=SE_a16_190712 SUBJECT_SAMPLE_FACTORS - SE_a17_190712 Class:I57 RAW_FILE_NAME=SE_a17_190712 SUBJECT_SAMPLE_FACTORS - SE_a18_190712 Class:I55 RAW_FILE_NAME=SE_a18_190712 SUBJECT_SAMPLE_FACTORS - SE_a20_190712 Class:I77 RAW_FILE_NAME=SE_a20_190712 #COLLECTION CO:COLLECTION_SUMMARY The Staphylococcus epidermidis 19N strain was collected from the anterior nares CO:COLLECTION_SUMMARY of a healthy person in Portugal in 2001. This strain was previously CO:COLLECTION_SUMMARY characterised by whole genome sequencing and belongs to clonal lineage B. A CO:COLLECTION_SUMMARY single colony from a S. epidermidis 19N strain culture grown O/N at 37ºC (TSA, CO:COLLECTION_SUMMARY BactoTM), was used to pre-inoculate Tryptic Soy Broth (TSB) medium with two CO:COLLECTION_SUMMARY different pH (5.5 and 7.4) that was incubated overnight at 37ºC under CO:COLLECTION_SUMMARY agitation. Pre-inoculums were adjusted either to pH 5.5 or pH 7.4, with CO:COLLECTION_SUMMARY hydrochloric acid. In this work, three pH transitions from pre-inoculum to CO:COLLECTION_SUMMARY inoculum were assayed. S. epidermidis pre-inoculums and the growth were CO:COLLECTION_SUMMARY performed at medium with pH 7.4, to mimic the blood pH; and pH 5.5, to mimic the CO:COLLECTION_SUMMARY skin pH. The pre-inoculum cellular density was adjusted to 0.06 (OD600) CO:COLLECTION_SUMMARY (aprox.1.5x108 CFU/mL) and used to inoculate fresh medium in the three CO:COLLECTION_SUMMARY conditions depicted in Figure 1, simulating S. epidermidis at skin and blood and CO:COLLECTION_SUMMARY a pH shock endured by S. epidermidis during the infection process from skin to CO:COLLECTION_SUMMARY blood transition. The cell cultures incubated at 37ºC with 225 rpm were CO:COLLECTION_SUMMARY followed by OD600 and recovered at mid-exponential phase for further analysis. CO:SAMPLE_TYPE Staphylococcus epidermidis intracellular CO:STORAGE_CONDITIONS -80℃ #TREATMENT TR:TREATMENT_SUMMARY n this work, three pH transitions from pre-inoculum to inoculum were assayed. S. TR:TREATMENT_SUMMARY epidermidis pre-inoculums and the growth were performed at medium with pH 7.4, TR:TREATMENT_SUMMARY to mimic the blood pH; and pH 5.5, to mimic the skin pH. The pre-inoculum TR:TREATMENT_SUMMARY cellular density was adjusted to 0.06 (OD600) (aprox.1.5x108 CFU/mL) and used to TR:TREATMENT_SUMMARY inoculate fresh medium in the three conditions depicted in Figure 1, simulating TR:TREATMENT_SUMMARY S. epidermidis at skin and blood and a pH shock endured by S. epidermidis during TR:TREATMENT_SUMMARY the infection process from skin to blood transition. The cell cultures incubated TR:TREATMENT_SUMMARY at 37ºC with 225 rpm were followed by OD600 and recovered at mid-exponential TR:TREATMENT_SUMMARY phase for further analysis. Pre-inocula were prepared in TSB medium at pH 5.5 or TR:TREATMENT_SUMMARY 7.4. Inocula at pH 5.5 was used for the cultures grown at 5.5 (N55) and 7.4 TR:TREATMENT_SUMMARY (N57), and the inoculum at pH 7.4 for the culture at the same pH (N77). The TR:TREATMENT_SUMMARY cells were harvested at mid-exponential phase. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Cells were recovered at mid-exponential phase from 100 mL cultures following a SP:SAMPLEPREP_SUMMARY protocol adapted from Somerville & Powers (Somerville and Powers 2014). Eight SP:SAMPLEPREP_SUMMARY biological replicates of each independent growth condition were obtained. Cells SP:SAMPLEPREP_SUMMARY were harvested by centrifugation at 5000 x g for 5 min at 4ºC. Cells were SP:SAMPLEPREP_SUMMARY washed with 20 mM phosphate buffer pH 7.2-7.4 and centrifuged for 1 min at SP:SAMPLEPREP_SUMMARY 13,000 rpm. Cell pellet was suspended in the same buffer with a final OD600 of SP:SAMPLEPREP_SUMMARY 20 and stored at -80ºC for further metabolite extraction. Cells were thawed in SP:SAMPLEPREP_SUMMARY a water bath at room temperature and 750 µL of 60% methanol were added and SP:SAMPLEPREP_SUMMARY subjected to three freeze-thaw cycles using liquid nitrogen. Extracted samples SP:SAMPLEPREP_SUMMARY were centrifuged at 21,000 g for 5 min at 4ºC. The extraction process on the SP:SAMPLEPREP_SUMMARY pellets was repeated twice. The supernatants were kept and stored together at SP:SAMPLEPREP_SUMMARY -20ºC overnight and dried in a SpeedVac. Dried samples were dissolved in: 750 SP:SAMPLEPREP_SUMMARY µL phosphate buffer (33 mM, pH 7.0 in D2O with 2 mM of sodium azide) with 0.21 SP:SAMPLEPREP_SUMMARY mM of 3-(trimethylsilyl)propionic-2,2,3,3-d4 (TSP). The suspensions were SP:SAMPLEPREP_SUMMARY centrifuged at 21,000 g for 5 min at 4ºC and the resulting supernatants were SP:SAMPLEPREP_SUMMARY then transferred to 5 mm NMR tubes. #ANALYSIS AN:ANALYSIS_TYPE NMR #NMR NM:INSTRUMENT_NAME Bruker Avance II+ 800 MHz NM:INSTRUMENT_TYPE FT-NMR NM:NMR_EXPERIMENT_TYPE 1D-1H NM:SPECTROMETER_FREQUENCY 800 NM:NMR_PROBE 5 mm TXI-Z H/C/N/-D NM:NMR_SOLVENT D2O NM:NMR_TUBE_SIZE 5 mm NM:SHIMMING_METHOD Topshim NM:CHEMICAL_SHIFT_REF_CPD TSP NM:TEMPERATURE 25 #NMR_METABOLITE_DATA NMR_METABOLITE_DATA:UNITS nanomoles NMR_METABOLITE_DATA_START Samples SE_18_190530 SE_23_190530 SE_24_190530 SE_a04_190712 SE_a07_190712 SE_a11_190712 SE_a18_190712 SE_10_190530 SE_11_190530 SE_4_190530 SE_7_190530 SE_a03_190712 SE_a09_190712 SE_a13_190712_rep SE_a17_190712 SE_1_190530 SE_5_190530 SE_6_190530 SE_9_190530 SE_a06_190712 SE_a12_190712 SE_a16_190712 SE_a20_190712 Factors Class:I55 Class:I55 Class:I55 Class:I55 Class:I55 Class:I55 Class:I55 Class:I57 Class:I57 Class:I57 Class:I57 Class:I57 Class:I57 Class:I57 Class:I57 Class:I77 Class:I77 Class:I77 Class:I77 Class:I77 Class:I77 Class:I77 Class:I77 2-Hydroxyisobutyrate 2.625 3.9 4.125 4.275 2.625 1.5 1.425 0.9 0.675 0.825 0.6 0.675 3.15 3.975 2.7 1.425 1.2 1.2 1.2 1.35 2.475 2.25 1.425 3-Hydroxyisovalerate 3.675 3.525 3.525 9.675 10.2 2.85 2.1 4.95 5.325 4.575 4.8 10.5 9.375 2.1 10.575 3.3 3.225 4.425 4.35 10.425 2.325 10.875 2.925 AMP 4.2 6.375 8.625 17.1 14.85 17.175 15.45 15.225 11.55 14.25 16.95 18.375 13.425 12.6 12.825 22.95 21.9 11.775 17.85 20.025 18.225 19.8 21.075 Acetate 43.875 35.175 67.425 65.775 58.65 53.175 59.775 30.3 36.525 43.8 32.775 39.825 51.9 39.75 37.95 61.125 48.9 54.6 52.275 71.4 125.025 116.025 75.75 Adenine 3.15 4.275 4.35 7.725 4.425 4.5 10.575 3.75 1.875 4.05 6.225 6.6 5.7 5.55 4.35 7.05 4.575 9.075 5.025 14.25 17.4 18.075 13.725 Adenosine 3.15 6.75 11.25 21.3 15.225 16.2 17.55 14.175 13.2 16.8 14.4 14.85 12.9 11.625 16.575 22.8 21.075 14.175 21.45 22.425 25.275 20.1 23.025 Alanine 10.275 20.1 27.15 50.7 47.475 40.2 54.675 33.675 23.475 22.275 36.9 39.9 24.825 24 35.025 111.825 42.9 36.3 51 73.65 101.925 87.975 83.325 Arabinose 1.65 4.35 3.6 9.525 5.625 7.275 8.175 0.75 2.25 3.6 2.85 3.975 4.125 1.65 3.525 11.175 14.625 19.125 11.25 13.65 12.3 24.225 13.95 Asparagine 13.425 19.5 24.6 19.95 17.625 14.1 19.725 11.175 8.1 14.1 11.85 18.075 8.7 12 10.05 12 13.95 13.725 18.75 18.675 13.8 14.55 21.375 Aspartate 94.875 116.1 139.425 190.65 167.175 191.925 170.475 254.1 263.025 331.125 327.225 368.4 194.775 201.975 240.6 154.65 180.9 142.725 149.4 206.1 163.35 187.425 241.5 Betaine 314.85 490.5 560.4 757.8 504.975 586.125 550.5 154.2 159.525 267.45 364.125 532.575 278.175 258.525 404.4 256.425 237.975 297.225 305.4 377.25 315.225 354.675 493.5 Choline 14.925 22.65 31.275 44.1 25.2 29.55 33.45 4.125 4.125 6.6 8.1 9.9 4.875 5.325 8.475 9.675 7.575 9.675 10.95 10.95 10.35 9.9 13.275 Coenzyme A 2.325 15.75 20.025 2.85 9.75 15.975 4.575 17.1 31.725 8.4 5.55 20.85 6.075 2.1 5.85 12 16.8 15.225 9.675 7.725 16.65 5.1 5.55 Cytidine monophosphate 3.675 5.55 7.35 30.9 24.45 21.45 22.35 13.2 8.325 11.025 13.725 20.325 11.775 10.275 18.375 25.575 14.7 12.9 25.05 32.175 27.3 29.85 31.425 Formate 22.05 23.25 22.65 105.6 100.275 92.55 84.075 18.525 23.55 21.675 23.85 65.625 71.175 67.65 86.85 25.8 23.925 23.475 18.675 65.775 56.7 47.1 56.1 Glucose 0 0 10.95 0 0 0 0 3.675 1.35 0 0 0 0 0 0 14.55 5.55 4.725 3.375 0 0 0 0 Glutamate 325.2 437.7 498.9 590.325 470.475 532.95 515.4 250.125 263.1 294.375 315.225 422.175 267.6 277.725 289.65 568.5 528.9 507.675 544.2 495 439.875 525.375 549.75 Glutamine 45.075 65.7 99.675 68.1 54.075 54.45 49.05 15.9 11.025 0 19.125 31.425 22.8 25.2 20.175 0 23.4 21.525 20.625 22.2 20.25 25.8 32.55 Glycine 0.375 0.45 25.65 0.75 0.75 0.375 0.75 0.675 0.9 0.9 0.75 0.9 1.425 1.2 1.8 7.8 7.5 1.425 0.9 1.95 1.2 2.175 2.025 Guanosine 1.125 1.575 1.35 3.525 3.3 3.75 4.575 4.35 3.225 7.875 6 5.55 3.3 3.15 5.025 6.675 8.775 6.75 10.35 5.4 3.45 5.55 5.325 Histidine 0.9 2.1 2.175 4.35 3.3 4.275 3.9 2.4 1.725 2.325 2.925 3.45 2.175 1.95 3.15 4.725 3.675 3.3 5.1 3.975 4.2 4.35 4.2 Isoleucine 1.5 2.775 4.05 4.5 2.625 3.225 2.55 1.95 1.725 2.625 3.075 3.45 1.95 2.25 2.475 5.4 3.75 3.45 4.2 3.525 5.025 4.125 4.8 Isovalerate 1.125 0.975 1.8 3.45 3.525 3.15 3.3 0.675 1.2 1.275 0.825 1.2 1.275 0.9 0.825 0.9 1.2 1.2 1.05 3.3 3.075 3.375 2.55 Lactate 6.9 25.95 28.8 29.25 6.975 24.75 6.45 11.325 13.425 10.275 12.9 6.375 24.525 12.45 9.975 64.875 19.2 26.625 33.45 17.4 90.15 36.15 28.5 Leucine 7.575 11.925 15.9 16.875 11.7 14.1 12.975 6.975 6.225 8.7 10.8 13.575 8.85 9.15 10.35 17.475 13.125 11.775 16.5 13.875 19.575 15.825 17.55 Lysine 4.725 7.425 8.25 12.45 9.15 11.85 17.7 11.55 8.925 13.875 13.8 13.05 7.125 8.025 12.975 24.975 19.575 18.375 21.3 20.775 22.95 21 20.475 NAD+ 11.55 11.55 17.7 3.3 10.875 11.55 13.95 14.7 14.925 19.05 14.7 15.525 11.475 11.175 12.075 18.75 20.55 17.175 21.9 2.025 16.275 14.175 3.9 NADP+ 3.3 2.925 4.5 2.4 2.775 2.325 3 4.725 4.575 6.75 4.8 5.175 4.275 3.825 4.65 5.55 6.525 5.625 7.275 4.65 4.95 5.025 5.25 Nicotinate 1.575 3.525 1.35 3.075 2.775 3 2.4 2.1 3.225 0 3.075 4.575 2.1 2.55 4.575 3.75 1.2 0.825 1.125 3.975 3.75 5.55 4.125 Phenylalanine 3.6 5.625 7.725 8.85 7.5 8.475 7.35 4.875 5.025 6.75 7.35 9.075 5.55 5.85 7.8 10.125 7.875 6.75 8.25 7.875 8.4 9.75 9.225 Phosphoenolpyruvic acid 7.875 10.65 8.775 10.35 8.1 8.025 5.625 5.475 5.7 9.225 11.475 6.525 4.725 3.6 7.125 9.525 8.25 9.375 10.875 12.45 9.675 8.4 11.25 Succinate 8.1 9.675 12.15 22.725 20.325 23.025 22.275 7.35 7.95 9.45 9.6 12.375 8.4 9.225 8.925 15.225 12.9 14.025 14.55 22.05 21.75 22.8 21.15 Sucrose 0 1.425 115.725 1.575 0.9 1.05 1.05 0 0 0 0 0 2.025 2.775 2.325 43.2 1.125 1.2 1.425 0 0 1.95 0 Threonine 3.225 6.675 17.775 23.1 9.9 4.95 2.55 2.4 3.375 2.175 3.225 3.3 1.65 2.025 1.8 4.725 6.975 5.025 8.925 2.85 7.95 6.75 9.3 Tryptophan 0 1.125 0 1.2 0.825 1.275 1.35 1.425 0 1.425 0.9 0.6 0 0.825 1.95 2.025 1.425 1.5 1.8 1.875 2.7 3.3 1.65 Tyrosine 0.375 0.6 0.75 1.875 1.125 1.5 1.2 0.75 0.9 0.45 0.9 2.025 0.825 1.125 1.725 2.025 0.975 1.2 1.65 1.875 2.4 3.3 2.25 UMP 2.925 1.8 3.525 14.025 11.55 11.85 11.775 7.95 5.4 6.15 9.45 12.075 5.625 4.8 9.9 11.85 7.2 8.625 11.775 11.1 9 11.625 13.725 Uracil 0.825 1.575 2.85 13.125 9.375 11.025 14.775 2.025 0.825 1.875 1.65 5.4 2.55 2.7 3.9 3.675 1.425 2.85 4.2 11.325 11.625 12.75 10.05 Uridine 0.75 1.575 2.475 3.975 4.125 4.5 6.375 3.525 2.175 2.475 3.6 3.675 2.4 2.25 3.75 5.475 2.4 5.25 5.625 3.9 6.675 4.875 5.025 Valine 2.4 3.975 6.225 9.3 7.125 8.475 6.75 2.925 2.7 3.75 4.725 5.55 2.925 3 3.825 7.35 5.4 5.1 6.075 6.75 7.725 6.75 7.5 sn-Glycero-3-phosphocholine 40.05 56.775 60.675 10.875 40.35 41.325 38.85 13.2 15.3 16.05 17.175 19.425 15.3 15.825 18.225 19.95 16.125 17.175 20.025 12.3 15.075 14.1 16.725 beta-Alanine 2.475 4.65 4.05 6.075 8.7 7.575 10.875 5.325 3.75 8.925 6.3 4.65 5.175 4.425 4.35 7.65 8.55 10.35 7.575 9.6 8.025 12.75 9.9 Cystathionine 0 0 0 0 3.825 4.125 0 9.6 9.3 9.225 10.275 26.25 25.8 22.95 24.825 11.55 11.1 9 9.225 12.45 14.4 12.675 14.4 NMR_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name RefMet Name/Standardized Name* WorkBench PubChem Kegg Id 2-Hydroxyisobutyrate 2-Hydroxyisobutyric acid ME545925 11671 NA 3-Hydroxyisovalerate 3-Hydroxyisovaleric acid ME545926 69362 C20827 Acetate Acetic acid ME545928 176 C00033 Adenine Adenine ME545929 190 C00147 Adenosine Adenosine ME545930 60961 C00212 Alanine Alanine ME545931 5950 C00041 AMP AMP ME545927 6083 C00020 Arabinose Arabinose ME545932 439195 C02479 Asparagine Asparagine ME545933 6267 C00152 Aspartate Aspartic acid ME545934 5960 C00049 beta-Alanine beta-Alanine ME545966 239 C00099 Betaine Betaine ME545935 247 C00719 Choline Choline ME545936 305 C00114 Coenzyme A Coenzyme A ME545937 87642 C00010 Cystathionine Cystathionine ME545967 439258 C02291 Cytidine monophosphate CMP ME545938 6131 C00055 Formate Formic acid ME545939 284 C00058 Glucose Glucose ME545940 5793 C00221 Glutamate Glutamic acid ME545941 33032 C00025 Glutamine Glutamine ME545942 5961 C00064 Glycine Glycine ME545943 750 C00037 Guanosine Guanosine ME545944 6802 C00387 Histidine Histidine ME545945 6274 C00135 Isoleucine Isoleucine ME545946 6306 C00407 Isovalerate Isovaleric acid ME545947 10430 C08262 Lactate Lactic acid ME545948 107689 C00186 Leucine Leucine ME545949 6106 C00123 Lysine Lysine ME545950 5962 C00047 NAD+ NAD+ ME545951 5893 C00003 NADP+ NADP+ ME545952 5886 C00006 Nicotinate Nicotinic acid ME545953 938 C00253 Phenylalanine Phenylalanine ME545954 6140 C00079 Phosphoenolpyruvic acid Phosphoenolpyruvic acid ME545955 1005 C00074 sn-Glycero-3-phosphocholine sn-Glycero-3-phosphocholine ME545965 71920 C00670 Succinate Succinic acid ME545956 1110 C00042 Sucrose Sucrose ME545957 5988 C00089 Threonine Threonine ME545958 6288 C00188 Tryptophan Tryptophan ME545959 6305 C00078 Tyrosine Tyrosine ME545960 6057 C00082 UMP UMP ME545961 6030 C00105 Uracil Uracil ME545962 1174 C00106 Uridine Uridine ME545963 6029 C00299 Valine Valine ME545964 6287 C00183 METABOLITES_END #END