#METABOLOMICS WORKBENCH amitch_20150902_9523331_mwtab.txt DATATRACK_ID:354 STUDY_ID:ST000243 ANALYSIS_ID:AN000379 PROJECT_ID:PR000196
VERSION 1
CREATED_ON 2016-09-17
#PROJECT
PR:PROJECT_TITLE Metabolomic-based investigation on the effects of antifungal agents in Candida
PR:PROJECT_SUMMARY Our aim is to determine the metabolic effects of increasing doses of an
PR:PROJECT_SUMMARY agent on C. albicans metabolism (untargeted, steady state metabolomics). We
PR:PROJECT_SUMMARY culture in vitro Candida cells to the mid-logarithmic growth in liquid media
PR:PROJECT_SUMMARY at 37°C and then inoculate biological replicates (1ml) onto 22mm
PR:PROJECT_SUMMARY filters under vocuum filtration in sterile conditions. Subsequently, isolates
PR:PROJECT_SUMMARY be cultivated to midlogarithmic phase of growth on the same agar (RPMI-1640) to
PR:PROJECT_SUMMARY the antifungal agent has been added at a range of concentrations to achieve
PR:PROJECT_SUMMARY equivalent to 0 MIC (no drug), 0.0625 MIC, 0.125 MIC, 0.25 MIC, 0.5 MIC and 1.0
PR:PROJECT_SUMMARY at 37°C. At mid-logarithmic phase of growth (12h) replicates will be
PR:PROJECT_SUMMARY quenched by immersion into a solvent mixture of 40% acetonitrile: 40% methanol:
PR:PROJECT_SUMMARY water precooled at -40°C. The resulting quenched isolate/solvent mixtrue will
PR:PROJECT_SUMMARY mechanically lysed by bead-beating with 0.1mm Zirconia beads in a tissue
PR:PROJECT_SUMMARY and then centrifuged to seperate out cell wall components. Supernatants will be
PR:PROJECT_SUMMARY and stored at -80°C until they will be sent to SECIM facility.
PR:INSTITUTE Weill Cornell Medical College
PR:DEPARTMENT Medicine/Infectious Diseases
PR:LAST_NAME Walsh
PR:FIRST_NAME Thomas
PR:ADDRESS -
PR:EMAIL thw2003@med.cornell.edu
PR:PHONE -
PR:FUNDING_SOURCE Southeastern Center for Integrated Metabolomics (SECIM) pilot and feasibility
PR:FUNDING_SOURCE NIH U24 DK097209
#STUDY
ST:STUDY_TITLE Metabolomic-based investigation on the effects of antifungal agents in Candida
ST:STUDY_TYPE in vitro study/drug dosage
ST:STUDY_SUMMARY Our aim is to determine the metabolic effects of increasing doses of an
ST:STUDY_SUMMARY agent on C. albicans metabolism (untargeted, steady state metabolomics). We
ST:STUDY_SUMMARY culture in vitro Candida cells to the mid-logarithmic growth in liquid media
ST:STUDY_SUMMARY at 37°C and then inoculate biological replicates (1ml) onto 22mm
ST:STUDY_SUMMARY filters under vocuum filtration in sterile conditions. Subsequently, isolates
ST:STUDY_SUMMARY be cultivated to midlogarithmic phase of growth on the same agar (RPMI-1640) to
ST:STUDY_SUMMARY the antifungal agent has been added at a range of concentrations to achieve
ST:STUDY_SUMMARY equivalent to 0 MIC (no drug), 0.0625 MIC, 0.125 MIC, 0.25 MIC, 0.5 MIC and 1.0
ST:STUDY_SUMMARY at 37°C. At mid-logarithmic phase of growth (12h) replicates will be
ST:STUDY_SUMMARY quenched by immersion into a solvent mixture of 40% acetonitrile: 40% methanol:
ST:STUDY_SUMMARY water precooled at -40°C. The resulting quenched isolate/solvent mixtrue will
ST:STUDY_SUMMARY mechanically lysed by bead-beating with 0.1mm Zirconia beads in a tissue
ST:STUDY_SUMMARY and then centrifuged to seperate out cell wall components. Supernatants will be
ST:STUDY_SUMMARY and stored at -80°C until they will be sent to SECIM facility.
ST:INSTITUTE University of Florida
ST:DEPARTMENT SECIM
ST:LAST_NAME Katragkou
ST:FIRST_NAME Aspasia
ST:ADDRESS -
ST:EMAIL ask2012@med.cornell.edu
ST:PHONE -
ST:NUM_GROUPS 96
#SUBJECT
SU:SUBJECT_TYPE Yeast cells
SU:SUBJECT_SPECIES Candida albicans
SU:TAXONOMY_ID 5476
SU:GENOTYPE_STRAIN SC5314
#SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS - EXP_1_0.0625MIC_1 :0.0625MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.0625MIC_2 :0.0625MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.0625MIC_3 :0.0625MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.0625MIC_4 :0.0625MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.0625MIC_5 :0.0625MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.0625MIC_6 :0.0625MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.0625MIC_7 :0.0625MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.0625MIC_8 :0.0625MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_2_0.0625MIC_1 :0.0625MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.0625MIC_2 :0.0625MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.0625MIC_3 :0.0625MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.0625MIC_4 :0.0625MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.0625MIC_5 :0.0625MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.0625MIC_6 :0.0625MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.0625MIC_7 :0.0625MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.0625MIC_8 :0.0625MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_1_0.125MIC_1 :0.125MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.125MIC_2 :0.125MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.125MIC_3 :0.125MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.125MIC_4 :0.125MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.125MIC_5 :0.125MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.125MIC_6 :0.125MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.125MIC_7 :0.125MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.125MIC_8 :0.125MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_2_0.125MIC_1 :0.125MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.125MIC_2 :0.125MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.125MIC_3 :0.125MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.125MIC_4 :0.125MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.125MIC_5 :0.125MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.125MIC_6 :0.125MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.125MIC_7 :0.125MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.125MIC_8 :0.125MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_1_0.25MIC_1 :0.25MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.25MIC_2 :0.25MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.25MIC_3 :0.25MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.25MIC_4 :0.25MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.25MIC_5 :0.25MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.25MIC_6 :0.25MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.25MIC_7 :0.25MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.25MIC_8 :0.25MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_2_0.25MIC_1 :0.25MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.25MIC_2 :0.25MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.25MIC_3 :0.25MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.25MIC_4 :0.25MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.25MIC_5 :0.25MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.25MIC_6 :0.25MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.25MIC_7 :0.25MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.25MIC_8 :0.25MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_1_0.5MIC_1 :0.5MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.5MIC_2 :0.5MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.5MIC_3 :0.5MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.5MIC_4 :0.5MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.5MIC_5 :0.5MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.5MIC_6 :0.5MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.5MIC_7 :0.5MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0.5MIC_8 :0.5MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_2_0.5MIC_1 :0.5MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.5MIC_2 :0.5MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.5MIC_3 :0.5MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.5MIC_4 :0.5MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.5MIC_5 :0.5MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.5MIC_6 :0.5MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.5MIC_7 :0.5MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0.5MIC_8 :0.5MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_1_1.0MIC_1 :1.0MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_1.0MIC_2 :1.0MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_1.0MIC_3 :1.0MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_1.0MIC_4 :1.0MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_1.0MIC_5 :1.0MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_1.0MIC_6 :1.0MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_1.0MIC_7 :1.0MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_1.0MIC_8 :1.0MIC | :1
SUBJECT_SAMPLE_FACTORS - EXP_2_1.0MIC_1 :1.0MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_1.0MIC_2 :1.0MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_1.0MIC_3 :1.0MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_1.0MIC_4 :1.0MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_1.0MIC_5 :1.0MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_1.0MIC_6 :1.0MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_1.0MIC_7 :1.0MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_1.0MIC_8 :1.0MIC | :2
SUBJECT_SAMPLE_FACTORS - EXP_1_0MIC_1 :no drug | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0MIC_2 :no drug | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0MIC_3 :no drug | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0MIC_4 :no drug | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0MIC_5 :no drug | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0MIC_6 :no drug | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0MIC_7 :no drug | :1
SUBJECT_SAMPLE_FACTORS - EXP_1_0MIC_8 :no drug | :1
SUBJECT_SAMPLE_FACTORS - EXP_2_0MIC_1 :no drug | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0MIC_2 :no drug | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0MIC_3 :no drug | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0MIC_4 :no drug | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0MIC_5 :no drug | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0MIC_6 :no drug | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0MIC_7 :no drug | :2
SUBJECT_SAMPLE_FACTORS - EXP_2_0MIC_8 :no drug | :2
#COLLECTION
CO:COLLECTION_SUMMARY Culture supernatants (appx. 1 ml from each replicate) will be removed and
CO:COLLECTION_SUMMARY at -80C
CO:SAMPLE_TYPE Cells
CO:VOLUMEORAMOUNT_COLLECTED 1 mL
CO:STORAGE_CONDITIONS -80C
#TREATMENT
TR:TREATMENT_SUMMARY Candida cells grown to the mid-logarithmic phase will be exposed in biological
TR:TREATMENT_SUMMARY (X8) to the antifungal agent (micafungin) to a range of concentrations
TR:TREATMENT_SUMMARY of the strain's MIC, Minimal Inhibitory Concentration) 0.0625MIC 0.125MIC
TR:TREATMENT_SUMMARY 0.5MIC 1.0MIC. No drug exposed Candida cells will serve as controls
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY -
SP:SAMPLEPREP_PROTOCOL_FILENAME Sample_Preparation_of_Cell_Lysates.pdf
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE Reversed phase
MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap
CH:COLUMN_NAME ACE Excel 2 C18-PFP (100 x 2.1mm, 2um)
CH:METHODS_FILENAME Metabolomics_LCMSProtocol.pdf;Appendix_A_-_Internal_Standard_Prep_GLCMS.pdf
CH:INTERNAL_STANDARD Appendix A - Internal Standard Prep GLCMS.pdf
#ANALYSIS
AN:ANALYSIS_TYPE MS
AN:LABORATORY_NAME Garrett Lab
AN:DETECTOR_TYPE Orbitrap
#MS
MS:MS_COMMENTS -
MS:INSTRUMENT_NAME Thermo Q Exactive Orbitrap
MS:INSTRUMENT_TYPE Orbitrap
MS:MS_TYPE ESI
MS:ION_MODE POSITIVE
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS Peak height
MS_METABOLITE_DATA_START
Samples EXP_1_0.0625MIC_1 EXP_1_0.0625MIC_2 EXP_1_0.0625MIC_3 EXP_1_0.0625MIC_4 EXP_1_0.0625MIC_5 EXP_1_0.0625MIC_6 EXP_1_0.0625MIC_7 EXP_1_0.0625MIC_8 EXP_2_0.0625MIC_1 EXP_2_0.0625MIC_2 EXP_2_0.0625MIC_3 EXP_2_0.0625MIC_4 EXP_2_0.0625MIC_5 EXP_2_0.0625MIC_6 EXP_2_0.0625MIC_7 EXP_2_0.0625MIC_8 EXP_1_0.125MIC_1 EXP_1_0.125MIC_2 EXP_1_0.125MIC_3 EXP_1_0.125MIC_4 EXP_1_0.125MIC_5 EXP_1_0.125MIC_6 EXP_1_0.125MIC_7 EXP_1_0.125MIC_8 EXP_2_0.125MIC_1 EXP_2_0.125MIC_2 EXP_2_0.125MIC_3 EXP_2_0.125MIC_4 EXP_2_0.125MIC_5 EXP_2_0.125MIC_6 EXP_2_0.125MIC_7 EXP_2_0.125MIC_8 EXP_1_0.25MIC_1 EXP_1_0.25MIC_2 EXP_1_0.25MIC_3 EXP_1_0.25MIC_4 EXP_1_0.25MIC_5 EXP_1_0.25MIC_6 EXP_1_0.25MIC_7 EXP_1_0.25MIC_8 EXP_2_0.25MIC_1 EXP_2_0.25MIC_2 EXP_2_0.25MIC_3 EXP_2_0.25MIC_4 EXP_2_0.25MIC_5 EXP_2_0.25MIC_6 EXP_2_0.25MIC_7 EXP_2_0.25MIC_8 EXP_1_0.5MIC_1 EXP_1_0.5MIC_2 EXP_1_0.5MIC_3 EXP_1_0.5MIC_4 EXP_1_0.5MIC_5 EXP_1_0.5MIC_6 EXP_1_0.5MIC_7 EXP_1_0.5MIC_8 EXP_2_0.5MIC_1 EXP_2_0.5MIC_2 EXP_2_0.5MIC_3 EXP_2_0.5MIC_4 EXP_2_0.5MIC_5 EXP_2_0.5MIC_6 EXP_2_0.5MIC_7 EXP_2_0.5MIC_8 EXP_1_1.0MIC_1 EXP_1_1.0MIC_2 EXP_1_1.0MIC_3 EXP_1_1.0MIC_4 EXP_1_1.0MIC_5 EXP_1_1.0MIC_6 EXP_1_1.0MIC_7 EXP_1_1.0MIC_8 EXP_2_1.0MIC_1 EXP_2_1.0MIC_2 EXP_2_1.0MIC_3 EXP_2_1.0MIC_4 EXP_2_1.0MIC_5 EXP_2_1.0MIC_6 EXP_2_1.0MIC_7 EXP_2_1.0MIC_8 EXP_1_0MIC_1 EXP_1_0MIC_2 EXP_1_0MIC_3 EXP_1_0MIC_4 EXP_1_0MIC_5 EXP_1_0MIC_6 EXP_1_0MIC_7 EXP_1_0MIC_8 EXP_2_0MIC_1 EXP_2_0MIC_2 EXP_2_0MIC_3 EXP_2_0MIC_4 EXP_2_0MIC_5 EXP_2_0MIC_6 EXP_2_0MIC_7 EXP_2_0MIC_8
Factors :0.0625MIC | :1 :0.0625MIC | :1 :0.0625MIC | :1 :0.0625MIC | :1 :0.0625MIC | :1 :0.0625MIC | :1 :0.0625MIC | :1 :0.0625MIC | :1 :0.0625MIC | :2 :0.0625MIC | :2 :0.0625MIC | :2 :0.0625MIC | :2 :0.0625MIC | :2 :0.0625MIC | :2 :0.0625MIC | :2 :0.0625MIC | :2 :0.125MIC | :1 :0.125MIC | :1 :0.125MIC | :1 :0.125MIC | :1 :0.125MIC | :1 :0.125MIC | :1 :0.125MIC | :1 :0.125MIC | :1 :0.125MIC | :2 :0.125MIC | :2 :0.125MIC | :2 :0.125MIC | :2 :0.125MIC | :2 :0.125MIC | :2 :0.125MIC |