{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002420","ANALYSIS_ID":"AN003941","VERSION":"1","CREATED_ON":"January 2, 2023, 8:55 pm"},

"PROJECT":{"PROJECT_TITLE":"Isobaric labeling metabolites CRC studies","PROJECT_TYPE":"MS relative quantitative analysis","PROJECT_SUMMARY":"Isobaric labeling-based relative quantification for the discovery of serum metabolite biomarkers associated with growing early colorectal adenomas","INSTITUTE":"University of Wisconsin - Madison","LAST_NAME":"Liu","FIRST_NAME":"Yuan","ADDRESS":"777 Highland ave, Madison, Wisconsin, 53705, USA","EMAIL":"liu788@wisc.edu","PHONE":"6089606939"},

"STUDY":{"STUDY_TITLE":"Colorectal cancer isobaric labeling for metabolite quantification","STUDY_SUMMARY":"A major challenge in reducing the death rate of colorectal cancer is to screen patients using low-invasive testing. Blood test shows a high compliance rate with reduced invasiveness. In this work, a multiplex isobaric tag labeling strategy coupled with mass spectrometry is adopted to relatively quantify primary and secondary amine-containing metabolites in serum for the discovery of metabolite biomarkers of colorectal cancer. Serum samples from patients at different risk statuses and colorectal cancer growth statuses are studied. Metabolite identification is based on accurate mass matching and/or retention time of labeled metabolite standards. We quantify 40 metabolites across all the serum samples, including 18 metabolites validated with standards. We find significantly decreased levels of threonine and asparagine in the patients with growing adenomas or high-risk adenomas (p < 0.05). Glutamine levels decrease in patients with adenomas of unknown growth status or high-risk adenomas. In contrast, arginine levels are elevated in patients with low-risk adenoma. Receiver operating characteristic analysis shows high sensitivity and specificity of these metabolites for detecting growing adenomas. Based on these results, we conclude that potential metabolite biomarkers identified here contribute to distinguishing colorectal patients with growing adenomas from normal individuals and patients with unknown growth status of adenomas.","INSTITUTE":"University of Wisconsin - Madison","LAST_NAME":"Liu","FIRST_NAME":"Yuan","ADDRESS":"777 Highland ave, Madison, Wisconsin, 53705, USA","EMAIL":"liu788@wisc.edu","PHONE":"6089606939"},

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"SUBJECT_SAMPLE_FACTORS":[
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"Sample ID":"N2",
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{
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"Sample ID":"N3",
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{
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{
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"Sample ID":"N5",
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"Additional sample data":{"m/z of reporter ion":"118","RAW_FILE_NAME":"G13_1.mzML"}
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{
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"Sample ID":"N7",
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},
{
"Subject ID":"-",
"Sample ID":"N8",
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"Additional sample data":{"m/z of reporter ion":"116","RAW_FILE_NAME":"G14_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"N9",
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},
{
"Subject ID":"-",
"Sample ID":"N10",
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{
"Subject ID":"-",
"Sample ID":"N11",
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},
{
"Subject ID":"-",
"Sample ID":"N12",
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"Additional sample data":{"m/z of reporter ion":"116","RAW_FILE_NAME":"G15_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"N13",
"Factors":{"classification_based on growth rate":"control","classification_based on risks":"control"},
"Additional sample data":{"m/z of reporter ion":"117","RAW_FILE_NAME":"G15_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"N14",
"Factors":{"classification_based on growth rate":"control","classification_based on risks":"control"},
"Additional sample data":{"m/z of reporter ion":"118","RAW_FILE_NAME":"G15_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"N15",
"Factors":{"classification_based on growth rate":"control","classification_based on risks":"control"},
"Additional sample data":{"m/z of reporter ion":"115","RAW_FILE_NAME":"G16_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"N16",
"Factors":{"classification_based on growth rate":"control","classification_based on risks":"control"},
"Additional sample data":{"m/z of reporter ion":"116","RAW_FILE_NAME":"G16_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"N17",
"Factors":{"classification_based on growth rate":"control","classification_based on risks":"control"},
"Additional sample data":{"m/z of reporter ion":"117","RAW_FILE_NAME":"G16_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"N18",
"Factors":{"classification_based on growth rate":"control","classification_based on risks":"control"},
"Additional sample data":{"m/z of reporter ion":"118","RAW_FILE_NAME":"G16_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"N19",
"Factors":{"classification_based on growth rate":"control","classification_based on risks":"control"},
"Additional sample data":{"m/z of reporter ion":"115","RAW_FILE_NAME":"G17_1.mzML"}
},
{
"Subject ID":"-",
"Sample ID":"N20",
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}
],
"COLLECTION":{"COLLECTION_SUMMARY":"Serum samples were thawed on ice and centrifuged at 2000 g for 10 min to remove particulates and debris. Molecular weight cut-off filters (MWCO, 3 kDa, Millipore Amicon Ultra, Burlington, MA) were prerinsed 3 times with optima water at 14000 g for 20 min. Twenty microliter serum supernatant from each sample was diluted in 380 µl water and added to the filter then centrifuged for 20 min at 14000 g. Flowthrough was collected. Then 400 µL water was added to the filter to rinse the sample. An additional rinse step was applied. All the flowthrough (about 1.2 mL) was combined and dried down in Speedvac and stored at −20 °C until labeling. For normalization, a pooled serum sample from screening normal individuals was also prepared. For labeling of serum samples, 40 µL activated DiLeu reagents were mixed with serum flowthrough dissolved in 10 µL 0.5 M TEAB and shaken for 2 h. After the reaction was quenched, 2.5 µL of each reaction mixture with different DiLeu tags were combined at 1: 1: 1: 1 ratio and mixed well. To compare the relative abundance of each set of 4-plex DiLeu labeled metabolites, one channel from each 4-plex combination was selected and combined with 118-DiLeu tag labeled pooled serum samples. Ten µL of the mixture was taken for drying down and desalted using SCX Ziptips. Samples were dissolved in 15 µL 0.1% FA and 3 µL was injected into LC-MS for data acquisition with 3 technical replicates.","COLLECTION_PROTOCOL_FILENAME":"methods.txt","SAMPLE_TYPE":"Blood (serum)"},

"TREATMENT":{"TREATMENT_SUMMARY":"Among the 23 patients carrying adenomas, 15 patients were classified histologically as high-risk and the remaining 8 patients were classified as low-risk cases. In the high-risk cases, 10 were classified as growing by longitudinal CTC analysis, one as static, and 4 as unknown growth status."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Serum samples were thawed on ice and centrifuged at 2000 g for 10 min to remove particulates and debris. Molecular weight cut-off filters (MWCO, 3 kDa, Millipore Amicon Ultra, Burlington, MA) were prerinsed 3 times with optima water at 14000 g for 20 min. Twenty microliter serum supernatant from each sample was diluted in 380 µl water and added to the filter then centrifuged for 20 min at 14000 g. Flowthrough was collected. Then 400 µL water was added to the filter to rinse the sample. An additional rinse step was applied. All the flowthrough (about 1.2 mL) was combined and dried down in Speedvac and stored at −20 °C until labeling. For normalization, a pooled serum sample from screening normal individuals was also prepared. For labeling of serum samples, 40 µL activated DiLeu reagents were mixed with serum flowthrough dissolved in 10 µL 0.5 M TEAB and shaken for 2 h. After the reaction was quenched, 2.5 µL of each reaction mixture with different DiLeu tags were combined at 1: 1: 1: 1 ratio and mixed well. To compare the relative abundance of each set of 4-plex DiLeu labeled metabolites, one channel from each 4-plex combination was selected and combined with 118-DiLeu tag labeled pooled serum samples. Ten µL of the mixture was taken for drying down and desalted using SCX Ziptips. Samples were dissolved in 15 µL 0.1% FA and 3 µL was injected into LC-MS for data acquisition with 3 technical replicates."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"Four-plex pooled samples were reconstituted in 0.1% formic acid before injection. The HPLC-MS/MS analysis was conducted using a Waters nanoACQUITY UPLC coupled with Thermo Q Exactive Orbitrap MS. The separation column was in-house made with an emitter tip and dimensions of 75 μm inner diameter × 15 cm length. The column was packed with 1.7 μm, 150 Å, ethylene-bridged-hybrid (BEH) C18 material (Waters, Milford, MA). Mobile phase A was water containing 0.1% formic acid, and mobile phase B was acetonitrile containing 0.1% formic acid. The flow rate was set as 0.3 μL/min, and the LC gradient was 55 min and set as follows: 0−10 min, 3%-30% solvent B; 10−30 min, 30−80% B; 30-30.5 min, 80%-95% B; 30.5− 40.5 min, 95% B; 40.5−41 min, 95%-3% B; 41-55 min, 3% B. Positive ionization mode was used and full MS scans were acquired from m/z 180 to 800 at a resolution of 60 k, automatic gain control (AGC) was set as 5x 10^5, and a maximum injection time as set as 30 ms. The top 20 precursors were selected for normalized collision energy (NCE) dissociation (NCE = 30) with an isolation window of m/z 1, fixed first m/z 110, dynamic exclusion of 5 seconds, charge exclusion of >2, and a resolution of 35 k.","CHROMATOGRAPHY_TYPE":"Reversed phase","INSTRUMENT_NAME":"Waters NanoAcquity","COLUMN_NAME":"Waters ACQUITY UPLC BEH C18 (150 mm x 75 μm, 1.7 μm, 150 Å)","SOLVENT_A":"100% water; 0.01% formic acid","SOLVENT_B":"100% acetonitrile; 0.01% formic acid","FLOW_GRADIENT":"LC gradient was 55 min and set as follows: 0−10 min, 3%-30% solvent B; 10−30 min, 30−80% B; 30-30.5 min, 80%-95% B; 30.5− 40.5 min, 95% B; 40.5−41 min, 95%-3% B; 41-55 min, 3% B.","FLOW_RATE":"0.3 μL/min","COLUMN_TEMPERATURE":"Room temperature"},

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

"MS":{"INSTRUMENT_NAME":"Thermo Q Exactive Orbitrap","INSTRUMENT_TYPE":"Orbitrap","MS_TYPE":"ESI","ION_MODE":"POSITIVE","MS_COMMENTS":"Positive ionization mode was used and full MS scans were acquired from m/z 180 to 800 at a resolution of 60 k, automatic gain control (AGC) was set as 5x 10^5, and a maximum injection time as set as 30 ms. The top 20 precursors were selected for normalized collision energy (NCE) dissociation (NCE = 30) with an isolation window of m/z 1, fixed first m/z 110, dynamic exclusion of 5 seconds, charge exclusion of >2, and a resolution of 35 k."},

"MS_METABOLITE_DATA":{
"Units":"1",

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"Metabolites":[{"Metabolite":"1-Methylhistidine","KEGG":"C01152","PubChem ID":"92105","quantitated m/z":"169.0839"},{"Metabolite":"2-Hydroxy-L-methionine","KEGG":"","PubChem ID":"45082566","quantitated m/z":"165.0454"},{"Metabolite":"5-Hydroxy-L-tryptophan","KEGG":"C00643","PubChem ID":"439280","quantitated m/z":"220.0845"},{"Metabolite":"Alanine","KEGG":"C00041","PubChem ID":"5950","quantitated m/z":"89.0471"},{"Metabolite":"Amino (2S)-2,5-diamino-5-oxopentanoate","KEGG":"","PubChem ID":"22417575","quantitated m/z":"161.0795"},{"Metabolite":"Aminoadipic acid","KEGG":"C00956","PubChem ID":"469","quantitated m/z":"161.0682"},{"Metabolite":"Arginine","KEGG":"C00062","PubChem ID":"6322","quantitated m/z":"174.1107"},{"Metabolite":"Asparagine","KEGG":"C00152","PubChem ID":"6267","quantitated m/z":"132.0531"},{"Metabolite":"Citrulline","KEGG":"C00327","PubChem ID":"9750","quantitated m/z":"175.0953"},{"Metabolite":"Creatine; Beta-Guanidinopropionic acid","KEGG":"C00300","PubChem ID":"586","quantitated m/z":"131.0689"},{"Metabolite":"Creatinine","KEGG":"C00791","PubChem ID":"588","quantitated m/z":"113.0585"},{"Metabolite":"Cystine","KEGG":"C00491","PubChem ID":"67678","quantitated m/z":"240.0239"},{"Metabolite":"Fructosyl-lysine","KEGG":"","PubChem ID":"9839580","quantitated m/z":"308.1573"},{"Metabolite":"Gamma-Glutamyltyrosine","KEGG":"","PubChem ID":"94340","quantitated m/z":"310.1163"},{"Metabolite":"Glutamic acid","KEGG":"C00025","PubChem ID":"33032","quantitated m/z":"147.0525"},{"Metabolite":"Glutamine","KEGG":"C00064","PubChem ID":"5961","quantitated m/z":"146.0687"},{"Metabolite":"Glutamylleucine","KEGG":"","PubChem ID":"9856500","quantitated m/z":"260.1369"},{"Metabolite":"Histidine","KEGG":"C00135","PubChem ID":"6274","quantitated m/z":"155.0692"},{"Metabolite":"Isoleucine","KEGG":"C00407","PubChem ID":"6306","quantitated m/z":"131.0942"},{"Metabolite":"Kynurenine","KEGG":"C00328","PubChem ID":"846","quantitated m/z":"208.0854"},{"Metabolite":"Leucine","KEGG":"C00123","PubChem ID":"6106","quantitated m/z":"131.0942"},{"Metabolite":"Lysine","KEGG":"C00047","PubChem ID":"5962","quantitated m/z":"146.1053"},{"Metabolite":"LysoPE(0:0/15:0)","KEGG":"","PubChem ID":"53480921","quantitated m/z":"439.2685"},{"Metabolite":"LysoPE(0:0/16:0)","KEGG":"","PubChem ID":"53480922","quantitated m/z":"453.2843"},{"Metabolite":"Methionine","KEGG":"C00073","PubChem ID":"6137","quantitated m/z":"149.0497"},{"Metabolite":"N-(1-Deoxy-1-fructosyl)tyrosine","KEGG":"","PubChem ID":"131752248","quantitated m/z":"343.1265"},{"Metabolite":"N-Fructosyl phenylalanine","KEGG":"","PubChem ID":"85152457","quantitated m/z":"327.1313"},{"Metabolite":"Nitrotyrosine","KEGG":"","PubChem ID":"9834478","quantitated m/z":"226.0588"},{"Metabolite":"Norophthalmic acid","KEGG":"","PubChem ID":"5489007","quantitated m/z":"275.1109"},{"Metabolite":"Ornithine","KEGG":"C00077","PubChem ID":"6262","quantitated m/z":"132.0898"},{"Metabolite":"Phenylalanine","KEGG":"C00079","PubChem ID":"6140","quantitated m/z":"165.0786"},{"Metabolite":"Phenylalanylglutamic acid","KEGG":"","PubChem ID":"151134","quantitated m/z":"294.1212"},{"Metabolite":"Phenylalanylphenylalanine","KEGG":"","PubChem ID":"65104","quantitated m/z":"312.1472"},{"Metabolite":"Phenylalanyl-Serine","KEGG":"","PubChem ID":"193508","quantitated m/z":"252.1107"},{"Metabolite":"Proline","KEGG":"C00148","PubChem ID":"145742","quantitated m/z":"115.0628"},{"Metabolite":"Threonine","KEGG":"C00188","PubChem ID":"6288","quantitated m/z":"119.0579"},{"Metabolite":"Tryptophan","KEGG":"C00078","PubChem ID":"6305","quantitated m/z":"204.0898"},{"Metabolite":"Tyrosine","KEGG":"C00082","PubChem ID":"6057","quantitated m/z":"181.0734"},{"Metabolite":"Uridine","KEGG":"C00299","PubChem ID":"6029","quantitated m/z":"244.0689"},{"Metabolite":"Valine","KEGG":"C00183","PubChem ID":"6287","quantitated m/z":"117.0785"}]
}

}