{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002409","ANALYSIS_ID":"AN003926","VERSION":"1","CREATED_ON":"12-16-2022"},
"PROJECT":{"PROJECT_TITLE":"Spatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract","PROJECT_SUMMARY":"Most utilization of human diets occurs in the small intestine, which remains largely unstudied. Here, we used a novel non-invasive, ingestible sampling device to probe the spatiotemporal variation of upper intestinal luminal contents during routine daily digestion in 15 healthy subjects. We analyzed 274 intestinal samples and 60 corresponding stool homogenates by combining five metabolomics assays and 16S rRNA sequencing. We identified 1,909 metabolites, including sulfonolipids and novel bile acids. Stool and intestinal metabolomes differed dramatically. Food metabolites displayed known differences and trends in dietary biomarkers, unexpected increases in dicarboxylic acids along the intestinal tract, and a positive association between luminal keto acids and fruit intake. Diet-derived and microbially linked metabolites accounted for the largest inter-subject differences. Interestingly, subjects exhibited large variation in levels of bioactive fatty acid esters of hydroxy fatty acids (FAHFAs) and sulfonolipids. Two subjects who had taken antibiotics within 6 months prior to sampling showed markedly different patterns in these and other microbially related metabolites; from this variation, we identified Blautia species as most likely to be involved in FAHFA metabolism. Thus, in vivo sampling of the human small intestine under physiologic conditions can reveal links between diet, host and microbial metabolism.","INSTITUTE":"UC Davis","LAST_NAME":"Folz","FIRST_NAME":"Jake","ADDRESS":"1 Shields Ave","EMAIL":"jfolz@ucdavis.edu","PHONE":"7155636311","DOI":"http://dx.doi.org/10.21228/M8G99R"},
"STUDY":{"STUDY_TITLE":"Spatial, temporal, and inter-subject variation of the metabolome along the human upper intestinal tract (MS RP positive data)","STUDY_SUMMARY":"Most utilization of human diets occurs in the small intestine, which remains largely unstudied. Here, we used a novel non-invasive, ingestible sampling device to probe the spatiotemporal variation of upper intestinal luminal contents during routine daily digestion in 15 healthy subjects. We analyzed 274 intestinal samples and 60 corresponding stool homogenates by combining five metabolomics assays and 16S rRNA sequencing. We identified 1,909 metabolites, including sulfonolipids and novel bile acids. Stool and intestinal metabolomes differed dramatically. Food metabolites displayed known differences and trends in dietary biomarkers, unexpected increases in dicarboxylic acids along the intestinal tract, and a positive association between luminal keto acids and fruit intake. Diet-derived and microbially linked metabolites accounted for the largest inter-subject differences. Interestingly, subjects exhibited large variation in levels of bioactive fatty acid esters of hydroxy fatty acids (FAHFAs) and sulfonolipids. Two subjects who had taken antibiotics within 6 months prior to sampling showed markedly different patterns in these and other microbially related metabolites; from this variation, we identified Blautia species as most likely to be involved in FAHFA metabolism. Thus, in vivo sampling of the human small intestine under physiologic conditions can reveal links between diet, host and microbial metabolism.","INSTITUTE":"UC Davis","LAST_NAME":"Folz","FIRST_NAME":"Jake","ADDRESS":"1 Shields Ave","EMAIL":"jfolz@ucdavis.edu","PHONE":"7155636311","SUBMIT_DATE":"2022-12-16"},
"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606"},
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"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1939.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1943",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1943.raw"}
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{
"Subject ID":"-",
"Sample ID":"1948",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1948.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1952",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1952.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1956",
"Factors":{"Treatment":"Capsule Type 4"},
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},
{
"Subject ID":"-",
"Sample ID":"1960",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1960.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1965",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1965.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1969",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1969.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1972",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1972.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1976",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1976.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1981",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1981.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1987",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1987.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1991",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1991.raw"}
},
{
"Subject ID":"-",
"Sample ID":"1996",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_1996.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2000",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2000.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2004",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2004.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2007",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2007.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2010",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2010.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2012",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2012.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2013",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2013.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2018",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2018.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2019",
"Factors":{"Treatment":"Capsule Type 4"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2019.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2126",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2126.raw"}
},
{
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"Sample ID":"2127",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2127.raw"}
},
{
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"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2130.raw"}
},
{
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},
{
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},
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},
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},
{
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"Factors":{"Treatment":"Stool"},
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},
{
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"Sample ID":"2150",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2150.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2151",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2151.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2159",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2159.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2161",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2161.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2162",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2162.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2164",
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},
{
"Subject ID":"-",
"Sample ID":"2165",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2165.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2166",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2166.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2167",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2167.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2168",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2168.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2169",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2169.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2170",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2170.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2171",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2171.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2172",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2172.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2173",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2173.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2174",
"Factors":{"Treatment":"Stool"},
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},
{
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"Factors":{"Treatment":"Stool"},
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},
{
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"Factors":{"Treatment":"Stool"},
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},
{
"Subject ID":"-",
"Sample ID":"2177",
"Factors":{"Treatment":"Stool"},
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},
{
"Subject ID":"-",
"Sample ID":"2178",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2178.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2179",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2179.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2180",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2180.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2181",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2181.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2195",
"Factors":{"Treatment":"Stool"},
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},
{
"Subject ID":"-",
"Sample ID":"2196",
"Factors":{"Treatment":"Stool"},
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},
{
"Subject ID":"-",
"Sample ID":"2197",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2197.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2198",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2198.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2199",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2199.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2200",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2200.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2201",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2201.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2475",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2475.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2476",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2476.raw"}
},
{
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"Sample ID":"2477",
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"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2477.raw"}
},
{
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"Sample ID":"2478",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2478.raw"}
},
{
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"Sample ID":"2479",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2479.raw"}
},
{
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"Sample ID":"2480",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2480.raw"}
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{
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"Sample ID":"2481",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2481.raw"}
},
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"Sample ID":"2482",
"Factors":{"Treatment":"Stool"},
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{
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"Sample ID":"2483",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2483.raw"}
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{
"Subject ID":"-",
"Sample ID":"2484",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2484.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2556",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2556.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2557",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2557.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2558",
"Factors":{"Treatment":"Stool"},
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},
{
"Subject ID":"-",
"Sample ID":"2559",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2559.raw"}
},
{
"Subject ID":"-",
"Sample ID":"2560",
"Factors":{"Treatment":"Stool"},
"Additional sample data":{"RAW_FILE_NAME":"CSHpos_021121_2560.raw"}
},
{
"Subject ID":"-",
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],
"COLLECTION":{"COLLECTION_SUMMARY":"The CapScan sampling devices (Envivo Bio Inc, San Carlos CA) were constructed with a coating designed to dissolve at a specific pH to take advantage of the pH gradient of the human intestine. After the coating dissolved, a compressed elastic bladder expanded to pull in 400 µL of luminal contents through a oneway valve. This valve remained sealed until recovery from stool. The pH coating of each capsule type Page 13/30 dissolved at pH 5.5 (type 1), 6 (type 2), or 7.5 (types 3 and 4). Type 4 also had a time delay to target the distal ileum or ascending colon. Four sampling capsules were swallowed 3 hours after lunch or dinner across 2 days (Figure 1A). Subjects were instructed to maintain their normal diet, record the time of any food or drink consumed over the testing period, and to not consume caffeinated beverages after lunch on sampling days. Detailed guidelines are provided in Supplemental Material. Stool was collected and immediately frozen at -20 °C until stool was thawed and filled capsule devices were retrieved. Liquid sample was removed from each bladder using a hypodermic needle. An aliquot of each sample was used for 16S rRNA gene sequencing while another aliquot was centrifuged at 10,000 rcf for 3 min, and the supernatant was used for metabolomics analysis.","SAMPLE_TYPE":"Intestine"},
"TREATMENT":{"TREATMENT_SUMMARY":"We aimed to comprehensively study metabolomic differences among luminal samples from the upper intestinal tract of 15 healthy subjects to better understand the extent of spatial and temporal variation and to gauge the prospects of integrating metabolome and microbiome data. Volunteers swallowed sets of 4 sampling devices per sampling timepoint. These ingestible sampling devices were comprised of a collapsed collection bladder capped by a one-way valve in a capsule treated with pH-sensitive coatings. The four types of capsules differed only in their enteric coating which dissolved at pH 5.5 (capsule 1), pH 6 (capsule 2), and pH 7.5 (capsules 3 and 4) (Figure 1A). The thickness and pH-responsiveness of the coating enabled sampling at specific locations of the intestinal tract after entry into the duodenum. The devices did not contain any electronics beyond a passive radio frequency identification chip for tracking purposes. Once the coatings dissolved, an elastic collection bladder expanded and collected up to 400 µL of luminal contents through vacuum suction. The one-way valve prevented loss of sample and contamination from downstream fluids. Stool samples were frozen at -20 °C and all capsules were recovered from the stool prior to analysis. Liquid contents were retrieved from capsules using hypodermic needles. Aliquots of the raw sample were used for 16S ribosomal RNA microbiome analyses and the supernatants from centrifugated samples were used for metabolomic studies."},
"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Extraction is carried out using a bi-phasic solvent system of cold methanol, methyl tert-butyl ether (MTBE), and water. In more detail, cold methanol (225 µL is added to a 5mg tissue sample aliquot, which is placed into a 1.5 mL Eppendorf tube. Then, 750 µL of cold MTBE is added, followed by vortexing for 10 s. and shaking for 6 min. at 4ºC. Phase separation is induced by adding 188 µL of mass spec-grade water. After vortexing for 20 s. the sample is centrifuged at 14,000 rpm for 2 min. The upper organic phase is collected in two 300 µL aliquots for lipid analysis polar layer is collected in two 125 µL aliquots for HILIC analysis. One is stored at -20ºC as a backup and the other is evaporated to dryness in a SpeedVac. Dried extracts are resuspended in acetonitrile."},
"CHROMATOGRAPHY":{"INSTRUMENT_NAME":"Thermo Vanquish","COLUMN_NAME":"CSH C18 column (100 mm length × 2.1 mm i.d.; 1.7-µm particle size)","COLUMN_TEMPERATURE":"65","FLOW_GRADIENT":"15% B from 0 to 0.6 min, 30% B by 2 min, 48% B by 2.5 min, 82% B by 11 min, 99% B from 11.5 to 12 min, and 15% B from 12.1 to 14.2 min","FLOW_RATE":"600 ul/min","SOLVENT_A":"90% acetonitrile/10% water; 0.1% formic acid; 10 mM ammonium formate","SOLVENT_B":"80% isopropanol/20% acetonitrile; 0.1% formic acid; 10 mM ammonium formate","CHROMATOGRAPHY_TYPE":"Reversed phase"},
"ANALYSIS":{"ANALYSIS_TYPE":"MS"},
"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive HF-X Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","MS_COMMENTS":"HESI source conditions are as follows: sheath gas flow 55, auxiliary gas flow 15, sweep gas flow 3, capillary temperature 275°C, S-lens RF level 50, auxiliary gas heater temperature 450 °C, and needle voltage 3500 V and -3500 V for positive and negative ionization mode, respectively. DDA MS/MS spectra were acquired for the top 4 ions. MS scans were collected with 60k resolving power from 120-1700 m/z, AGC target of 106 ions, and maximum accumulation time of 100 ms. MS/MS spectra were collected with 15k resolving power, 1 Da isolation window, normalized collision energy of 20, 30, 60, 2 s dynamic exclusion window, 8×103 AGC target, and 50 ms maximum accumulation time. Spectra were stored in centroid mode. Three rounds of iterative exclusion MS/MS were acquired for each pooled QC sample.","ION_MODE":"POSITIVE"},
"MS_METABOLITE_DATA":{
"Units":"peak height",
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