{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002046","ANALYSIS_ID":"AN003331","VERSION":"1","CREATED_ON":"January 4, 2022, 1:58 am"},

"PROJECT":{"PROJECT_TITLE":"A Taguchi Design of Experiments Approach for Untargeted Metabolomics Sample Preparation Optimization","PROJECT_TYPE":"Design of Experiments - Sample preparation optimization","PROJECT_SUMMARY":"We describe an efficient Taguchi method design of experiments (DOE) approach to optimize the extraction solvent and volume, extraction time, and LC reconstitution solvent for a sequential non-polar and polar Caenorhabditis elegans extraction. DOE is rarely used in metabolomics yet provides a systematic approach for optimizing sample preparation while simultaneously decreasing the number of experiments required to obtain high-quality data.","INSTITUTE":"University of Georgia","DEPARTMENT":"Chemistry, Biochemistry, Complex Carbohydrate Research Center","LABORATORY":"Edison Lab","LAST_NAME":"Garcia","FIRST_NAME":"Brianna","ADDRESS":"315 Riverbend Road, Athens, GA, 30602, USA","EMAIL":"brianna.garcia@uga.edu","PHONE":"6269059945","FUNDING_SOURCE":"NIH Metabolomics Common Fund","CONTRIBUTORS":"Goncalo J. Gouveia, Amanda O. Shaver, I. Jonathan Amster, Arthur S. Edison, Franklin E. Leach III"},

"STUDY":{"STUDY_TITLE":"A Taguchi Design of Experiments Approach for Untargeted Metabolomics Sample Preparation Optimization","STUDY_TYPE":"Design of Experiments - Extraction Optimization","STUDY_SUMMARY":"We describe an efficient Taguchi method design of experiments (DOE) approach to optimize the extraction solvent and volume, extraction time, and LC reconstitution solvent for a sequential non-polar and polar Caenorhabditis elegans extraction. DOE is rarely used in metabolomics yet provides a systematic approach for optimizing sample preparation while simultaneously decreasing the number of experiments required to obtain high-quality data.","INSTITUTE":"University of Georgia","LAST_NAME":"Garcia","FIRST_NAME":"Brianna","ADDRESS":"315 Riverbend Road","EMAIL":"brianna.garcia@uga.edu","PHONE":"6269059945","NUM_GROUPS":"10","TOTAL_SUBJECTS":"30"},

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"Additional sample data":{"RAW_FILE_NAME":"aos456_ga_ms29_HLC_06.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp10_hilic_pos_02",
"Factors":{"sample_type":"Sample","experiment_number":"10","lc_ms_method":"hilic_pos"},
"Additional sample data":{"RAW_FILE_NAME":"aos456_ga_ms30_HLC_07.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp10_hilic_pos_03",
"Factors":{"sample_type":"Sample","experiment_number":"10","lc_ms_method":"hilic_pos"},
"Additional sample data":{"RAW_FILE_NAME":"aos456_ga_ms31_HLC_08.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp1_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"1","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_01_neg_15.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp1_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"1","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_02_neg_11.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp1_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"1","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_03_neg_36.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp2_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"2","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_05_neg_16.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp2_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"2","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_06_neg_20.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp2_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"2","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_07_neg_35.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp3_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"3","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_09_neg_10.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp3_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"3","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_10_neg_41.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp3_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"3","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_11_neg_31.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp4_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"4","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_13_neg_23.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp4_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"4","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_14_neg_17.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp4_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"4","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_15_neg_12.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp5_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"5","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_17_neg_27.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp5_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"5","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_18_neg_39.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp5_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"5","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_19_neg_32.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp6_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"6","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_21_neg_43.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp6_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"6","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_22_neg_25.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp6_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"6","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_23_neg_34.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp7_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"7","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_25_neg_26.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp7_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"7","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_26_neg_42.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp7_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"7","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_27_neg_28.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp8_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"8","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_29_neg_37.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp8_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"8","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_30_neg_46.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp8_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"8","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_31_neg_13.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp9_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"9","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_33_neg_45.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp9_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"9","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_34_neg_19.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp9_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"9","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos470_doeV3_35_neg_14.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp10_hilic_neg_01",
"Factors":{"sample_type":"Sample","experiment_number":"10","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos456_ga_ms29_HLC_neg_20.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp10_hilic_neg_02",
"Factors":{"sample_type":"Sample","experiment_number":"10","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos456_ga_ms30_HLC_neg_21.raw"}
},
{
"Subject ID":"-",
"Sample ID":"exp10_hilic_neg_03",
"Factors":{"sample_type":"Sample","experiment_number":"10","lc_ms_method":"hilic_neg"},
"Additional sample data":{"RAW_FILE_NAME":"aos456_ga_ms31_HLC_neg_22.raw"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"C. elegans were grown on large-scale culture plates (LSCPs), manually counted, aliquoted into 50,000 worm tubes, lyophilized and weighed. See detailed protocol for worm growth at: Shaver, A. O., Gouveia, G. J., Kirby, P. S., Andersen, E. C., Edison, A. S. Culture and Assay of Large-Scale Mixed-Stage Caenorhabditis elegans Populations. J. Vis. Exp. (171), e61453, doi:10.3791/61453 (2021).","SAMPLE_TYPE":"Worms","STORAGE_CONDITIONS":"-80℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"The compared groups are different extraction protocols using a Taguchi Design of Experiments (DOE) approach. Detailed information on the different extraction protocols compared is available in detail in the manuscript."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Samples were extracted according to the L9 orthogonal array described in the manuscript. Details are shown in the attached methods, but for full context refer to the manuscript."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"The following gradient program was used: -5.0 20% B; 0.0 min 20% B; 1.0 min 60% B; 5.0 min 70% B; 5.5 min 85% B; 8.0 min 90% B; 8.2-10.5 min 100% B; 10.7-12.0 min 20% B. A curve 5 value was set for -5.0 and 0.0 minutes, and a curve 6 for the remainder of the gradient.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"Thermo Scientific Accucore C30, 2.1 x 150 mm, 2.6 μm particle size","FLOW_RATE":"0.400 mL/min","COLUMN_TEMPERATURE":"55","SOLVENT_A":"40/60 water/acetonitrile, 10 mM ammonium formate, 0.1% formic acid","SOLVENT_B":"10/90 acetonitrile/2-propanol, 10 mM ammonium formate, 0.1% formic acid","SAMPLE_INJECTION":"2.0 uL"},

"ANALYSIS":{"ANALYSIS_TYPE":"MS","LABORATORY_NAME":"Edison Lab","OPERATOR_NAME":"Brianna M. Garcia","DETECTOR_TYPE":"Orbitrap","DATA_FORMAT":".raw"},

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF-X Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"NEGATIVE","MS_COMMENTS":"Scan range 150-2000 m/z. Details in attached methods. MZmine 2.53 was used for data processing.","CAPILLARY_TEMPERATURE":"262.50","DRY_GAS_FLOW":"50","DRY_GAS_TEMP":"425.0","SOURCE_TEMPERATURE":"425.0","SPRAY_VOLTAGE":"2500","DATAFORMAT":".raw Profile","MS_RESULTS_FILE":"ST002046_AN003331_Results.txt UNITS:Peak height Has m/z:Yes Has RT:Yes RT units:Minutes"}

}