{
"METABOLOMICS WORKBENCH":{"STUDY_ID":"ST002082","ANALYSIS_ID":"AN003397","VERSION":"1","CREATED_ON":"02-08-2024"},

"PROJECT":{"PROJECT_TITLE":"Predicting dying: a study of the metabolic changes and the dying process in patients with lung cancer","PROJECT_SUMMARY":"Background: Accurately recognising that a person may be dying is central for improving their experience of care. Yet recognising dying is difficult and predicting dying frequently inaccurate. Methods: Serial urine samples from patients (n=112) with lung cancer were analysed using high resolution untargeted mass spectrometry. ANOVA and volcano plot analysis demonstrated metabolites that changed in the last weeks of life. Further analysis identified potential biological pathways affected. Cox lasso logistic regression was engaged to develop a multivariable model predicting the probability of survival within the last 30 days of life. Results: In total 124 metabolites changed. ANOVA analysis identified 93 metabolites and volcano plot analysis 85 metabolites. 53 metabolites changed using both approaches. Pathways altered in the last weeks included those associated with decreased oral intake, muscle loss, decreased RNA and protein synthesis, mitochondrial dysfunction, disrupted β-oxidation and one carbon metabolism. Epinephrine and cortisol increased in the last 2 weeks and week respectively. A model predicting time to death using 7 metabolites had excellent accuracy (AUC= 0.86 at day 30, 0.88 at day 20 and 0.85 at day 10) and enabled classification of patients at low, medium and high risk of dying on a Kaplan-Meier survival curve. Conclusions: Metabolomic analysis identified metabolites and their associated pathways that change in the last weeks and days of life in patients with lung cancer. Prognostic tests based on the metabolites identified have the potential to change clinical practice and improve the care of dying patients.","INSTITUTE":"University of Liverpool Institute of Life Course Medical Sciences","LAST_NAME":"Norman","FIRST_NAME":"Brendan","ADDRESS":"William Henry Duncan Building, 6 West Derby Street, Liverpool, Merseyside, L7 8TX, United Kingdom","EMAIL":"bnorman@liv.ac.uk","PHONE":"(+44)151 794 9064","FUNDING_SOURCE":"This research received a Wellcome Trust Seed award for Science (202022/Z/16/Z) and a North West Cancer Research award (SI2018.11)","DOI":"http://dx.doi.org/10.21228/M8TT44","CONTRIBUTORS":"Séamus Coyle, Elinor Chapman, David Hughes, James Baker, Andrew S Davison, Brendan P Norman, Amara Callistus Nwosu, Mark Boyd, Catriona R Mayland, Stephen Mason, John Ellershaw, Chris Probert"},

"STUDY":{"STUDY_TITLE":"Predicting dying: a study of the metabolic changes and the dying process in patients with lung cancer","STUDY_TYPE":"Observational study","STUDY_SUMMARY":"Background: Accurately recognising that a person may be dying is central for improving their experience of care. Yet recognising dying is difficult and predicting dying frequently inaccurate. Methods: Serial urine samples from patients (n=112) with lung cancer were analysed using high resolution untargeted mass spectrometry. ANOVA and volcano plot analysis demonstrated metabolites that changed in the last weeks of life. Further analysis identified potential biological pathways affected. Cox lasso logistic regression was engaged to develop a multivariable model predicting the probability of survival within the last 30 days of life. Results: In total 124 metabolites changed. ANOVA analysis identified 93 metabolites and volcano plot analysis 85 metabolites. 53 metabolites changed using both approaches. Pathways altered in the last weeks included those associated with decreased oral intake, muscle loss, decreased RNA and protein synthesis, mitochondrial dysfunction, disrupted β-oxidation and one carbon metabolism. Epinephrine and cortisol increased in the last 2 weeks and week respectively. A model predicting time to death using 7 metabolites had excellent accuracy (AUC= 0.86 at day 30, 0.88 at day 20 and 0.85 at day 10) and enabled classification of patients at low, medium and high risk of dying on a Kaplan-Meier survival curve. Conclusions: Metabolomic analysis identified metabolites and their associated pathways that change in the last weeks and days of life in patients with lung cancer. Prognostic tests based on the metabolites identified have the potential to change clinical practice and improve the care of dying patients.","INSTITUTE":"University of Liverpool Institute of Life Course & Medical Sciences","LAST_NAME":"Norman","FIRST_NAME":"Brendan","ADDRESS":"William Henry Duncan Building, 6 West Derby Street, Liverpool, UK. L7 8TX","EMAIL":"bnorman@liverpool.ac.uk","PHONE":"(+44)151 794 9064","SUBMIT_DATE":"2022-01-24"},

"SUBJECT":{"SUBJECT_TYPE":"Human","SUBJECT_SPECIES":"Homo sapiens","TAXONOMY_ID":"9606","AGE_OR_AGE_RANGE":"47-89 years","GENDER":"Male and female","HUMAN_INCLUSION_CRITERIA":"Patients with lung cancer"},
"SUBJECT_SAMPLE_FACTORS":[
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"Sample ID":"D0D1_A-09_2017-11-21",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.95","RAW_FILE_NAME":"D0D1_A-09_2017-11-21.d"}
},
{
"Subject ID":"-",
"Sample ID":"D0D1_A-63_2018-03-28",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.09","RAW_FILE_NAME":"D0D1_A-63_2018-03-28.d"}
},
{
"Subject ID":"-",
"Sample ID":"D0D1_C-04_2017-08-10",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.36","RAW_FILE_NAME":"D0D1_C-04_2017-08-10.d"}
},
{
"Subject ID":"-",
"Sample ID":"D0D1_MC-05_2017-08-16",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"7.78","RAW_FILE_NAME":"D0D1_MC-05_2017-08-16.d"}
},
{
"Subject ID":"-",
"Sample ID":"D0D1_R-26_2018-04-20",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"14.93","RAW_FILE_NAME":"D0D1_R-26_2018-04-20.d"}
},
{
"Subject ID":"-",
"Sample ID":"D0D1_R-29_2018-06-01",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"14.08","RAW_FILE_NAME":"D0D1_R-29_2018-06-01.d"}
},
{
"Subject ID":"-",
"Sample ID":"D0D1_R-32_2018-07-13",
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"Additional sample data":{"Urine creatinine (mmol/L)":"3.52","RAW_FILE_NAME":"D0D1_R-32_2018-07-13.d"}
},
{
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"Factors":{"Time before death (weeks)":"1"},
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},
{
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"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"15.56","RAW_FILE_NAME":"D0D1_WHI-003_2018-04-16.d"}
},
{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"1"},
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},
{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"1"},
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{
"Subject ID":"-",
"Sample ID":"D2D16_A-57_2017-08-22",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.69","RAW_FILE_NAME":"D2D16_A-57_2017-08-22.d"}
},
{
"Subject ID":"-",
"Sample ID":"D2D16_MC-11_2018-07-01",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"7.21","RAW_FILE_NAME":"D2D16_MC-11_2018-07-01.d"}
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{
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},
{
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"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"10.08","RAW_FILE_NAME":"D2D16_WHI-015-107_2018-07-20.d"}
},
{
"Subject ID":"-",
"Sample ID":"G1_PS-A-05_03-03-2017",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"10.3","RAW_FILE_NAME":"G1_PS-A-05_03-03-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"G1_PS-A-51_21-11-2017",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.8","RAW_FILE_NAME":"G1_PS-A-51_21-11-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"G1_PS-MC-06_14-08-2017",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"3","RAW_FILE_NAME":"G1_PS-MC-06_14-08-2017.d"}
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{
"Subject ID":"-",
"Sample ID":"G1_PS-R-02_11-10-2016",
"Factors":{"Time before death (weeks)":"1"},
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{
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"Factors":{"Time before death (weeks)":"1"},
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"Sample ID":"G1_PS-WHI-020_15-06-2018",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"8.7","RAW_FILE_NAME":"G1_PS-WHI-020_15-06-2018.d"}
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{
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"Sample ID":"G2_PS-MC-02_03-07-2017",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.1","RAW_FILE_NAME":"G2_PS-MC-02_03-07-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"G2_PS-R-09_01-11-2016",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"4.5","RAW_FILE_NAME":"G2_PS-R-09_01-11-2016.d"}
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{
"Subject ID":"-",
"Sample ID":"G2_PS-R-21_15-11-2017",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"1.5","RAW_FILE_NAME":"G2_PS-R-21_15-11-2017.d"}
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"Sample ID":"G2_PS-WHI-027_04-09-2018",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.9","RAW_FILE_NAME":"G2_PS-WHI-027_04-09-2018.d"}
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"Sample ID":"G3_PS-WHI-101_11-04-2018",
"Factors":{"Time before death (weeks)":"1"},
"Additional sample data":{"Urine creatinine (mmol/L)":"16.3","RAW_FILE_NAME":"G3_PS-WHI-101_11-04-2018.d"}
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"Factors":{"Time before death (weeks)":"12+"},
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"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"1.75","RAW_FILE_NAME":"A-11_2018-05-17.d"}
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"Subject ID":"-",
"Sample ID":"A-12_2017-03-16",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"23.07","RAW_FILE_NAME":"A-12_2017-03-16.d"}
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"Subject ID":"-",
"Sample ID":"A-15_2018-06-06",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"14.76","RAW_FILE_NAME":"A-15_2018-06-06.d"}
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"Subject ID":"-",
"Sample ID":"A-20_2017-11-21",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"3.62","RAW_FILE_NAME":"A-20_2017-11-21.d"}
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"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"29.65","RAW_FILE_NAME":"A-21_2018-01-24.d"}
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"Sample ID":"A-24_2017-07-06",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"16.64","RAW_FILE_NAME":"A-24_2017-07-06.d"}
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{
"Subject ID":"-",
"Sample ID":"A-33_2017-12-12",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"15.89","RAW_FILE_NAME":"A-33_2017-12-12.d"}
},
{
"Subject ID":"-",
"Sample ID":"A-40_2018-07-24",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.33","RAW_FILE_NAME":"A-40_2018-07-24.d"}
},
{
"Subject ID":"-",
"Sample ID":"A-47_2017-08-02",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"7.63","RAW_FILE_NAME":"A-47_2017-08-02.d"}
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{
"Subject ID":"-",
"Sample ID":"A-48_2017-06-29",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"4.39","RAW_FILE_NAME":"A-48_2017-06-29.d"}
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{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"1.92","RAW_FILE_NAME":"A-49_2017-06-28.d"}
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{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"138","RAW_FILE_NAME":"A-61_2018-03-15.d"}
},
{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"19.97","RAW_FILE_NAME":"C-02_2017-03-16.d"}
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{
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"Factors":{"Time before death (weeks)":"12+"},
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{
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"Factors":{"Time before death (weeks)":"12+"},
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},
{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"12+"},
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{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"12+"},
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},
{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"12+"},
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{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"12+"},
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},
{
"Subject ID":"-",
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"Factors":{"Time before death (weeks)":"12+"},
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},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-A-06_20-07-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"12.9","RAW_FILE_NAME":"LCC_PS-A-06_20-07-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-A-07_02-03-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"1.3","RAW_FILE_NAME":"LCC_PS-A-07_02-03-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-A-08_26-07-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"21.6","RAW_FILE_NAME":"LCC_PS-A-08_26-07-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-A-13_06-07-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"4.8","RAW_FILE_NAME":"LCC_PS-A-13_06-07-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-A-19_06-07-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"18.6","RAW_FILE_NAME":"LCC_PS-A-19_06-07-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-A-32_06-07-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.9","RAW_FILE_NAME":"LCC_PS-A-32_06-07-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-A-50_29-06-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"3.8","RAW_FILE_NAME":"LCC_PS-A-50_29-06-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-C-01_09-03-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.4","RAW_FILE_NAME":"LCC_PS-C-01_09-03-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-C-12_01-06-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"7.6","RAW_FILE_NAME":"LCC_PS-C-12_01-06-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-MC-09_19-10-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"3.9","RAW_FILE_NAME":"LCC_PS-MC-09_19-10-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-MC-14_27-02-2018",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"11.6","RAW_FILE_NAME":"LCC_PS-MC-14_27-02-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-R-15_31-03-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.5","RAW_FILE_NAME":"LCC_PS-R-15_31-03-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-R-22_08-12-2017",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.3","RAW_FILE_NAME":"LCC_PS-R-22_08-12-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-R-24_11-01-2018",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"10.6","RAW_FILE_NAME":"LCC_PS-R-24_11-01-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-WHI-002_14-03-2018",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.4","RAW_FILE_NAME":"LCC_PS-WHI-002_14-03-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"LCC_PS-WHI-008_16-04-2018",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"7.7","RAW_FILE_NAME":"LCC_PS-WHI-008_16-04-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"MC-15_2018-09-19",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"11.93","RAW_FILE_NAME":"MC-15_2018-09-19.d"}
},
{
"Subject ID":"-",
"Sample ID":"MC-16_2018-09-12",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"4.27","RAW_FILE_NAME":"MC-16_2018-09-12.d"}
},
{
"Subject ID":"-",
"Sample ID":"MC-17_2018-09-12",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"8.2","RAW_FILE_NAME":"MC-17_2018-09-12.d"}
},
{
"Subject ID":"-",
"Sample ID":"R-30_2018-06-07",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"13.07","RAW_FILE_NAME":"R-30_2018-06-07.d"}
},
{
"Subject ID":"-",
"Sample ID":"WHI-016_2018-08-30",
"Factors":{"Time before death (weeks)":"12+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.5","RAW_FILE_NAME":"WHI-016_2018-08-30.d"}
},
{
"Subject ID":"-",
"Sample ID":"D2D16_A-18_2017-04-04",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"7.48","RAW_FILE_NAME":"D2D16_A-18_2017-04-04.d"}
},
{
"Subject ID":"-",
"Sample ID":"D2D16_A-56_2017-08-23",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"3.82","RAW_FILE_NAME":"D2D16_A-56_2017-08-23.d"}
},
{
"Subject ID":"-",
"Sample ID":"D2D16_WHI-014_2018-06-05",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"10.27","RAW_FILE_NAME":"D2D16_WHI-014_2018-06-05.d"}
},
{
"Subject ID":"-",
"Sample ID":"D2D16_WHI-023_2018-08-29",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.03","RAW_FILE_NAME":"D2D16_WHI-023_2018-08-29.d"}
},
{
"Subject ID":"-",
"Sample ID":"D2D16_WHI-026_2018-07-19",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.04","RAW_FILE_NAME":"D2D16_WHI-026_2018-07-19.d"}
},
{
"Subject ID":"-",
"Sample ID":"G3_PS-A-14_26-06-2017",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"3.8","RAW_FILE_NAME":"G3_PS-A-14_26-06-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"G3_PS-C-17_20-06-2017",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"2.5","RAW_FILE_NAME":"G3_PS-C-17_20-06-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"G3_PS-R-12_02-03-2017",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"2.3","RAW_FILE_NAME":"G3_PS-R-12_02-03-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"G4_PS-A-62_15-02-2018",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.2","RAW_FILE_NAME":"G4_PS-A-62_15-02-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"G4_PS-MC-10_06-03-2018",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"9","RAW_FILE_NAME":"G4_PS-MC-10_06-03-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"G4_PS-R-05_17-08-2016",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"4.6","RAW_FILE_NAME":"G4_PS-R-05_17-08-2016.d"}
},
{
"Subject ID":"-",
"Sample ID":"G4_PS-R-17_14-06-2017",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"8.9","RAW_FILE_NAME":"G4_PS-R-17_14-06-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"G4_PS-WHI-012_01-05-2018",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"7","RAW_FILE_NAME":"G4_PS-WHI-012_01-05-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"G5_PS-MC-07_14-08-2017",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"1.4","RAW_FILE_NAME":"G5_PS-MC-07_14-08-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"G5_PS-MC-13_27-02-2018",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"7","RAW_FILE_NAME":"G5_PS-MC-13_27-02-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"G5_PS-R-01_15-06-2016",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"1.5","RAW_FILE_NAME":"G5_PS-R-01_15-06-2016.d"}
},
{
"Subject ID":"-",
"Sample ID":"Group 4_PS-R-18_20-06-2017",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"9.7","RAW_FILE_NAME":"Group 4_PS-R-18_20-06-2017.d"}
},
{
"Subject ID":"-",
"Sample ID":"R-13_2018-04-23",
"Factors":{"Time before death (weeks)":"2"},
"Additional sample data":{"Urine creatinine (mmol/L)":"10.71","RAW_FILE_NAME":"R-13_2018-04-23.d"}
},
{
"Subject ID":"-",
"Sample ID":"D17_A-64_2018-07-06",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.37","RAW_FILE_NAME":"D17_A-64_2018-07-06.d"}
},
{
"Subject ID":"-",
"Sample ID":"D17_R-20_2017-11-22",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"11.61","RAW_FILE_NAME":"D17_R-20_2017-11-22.d"}
},
{
"Subject ID":"-",
"Sample ID":"D17_R-23_2017-12-13",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.6","RAW_FILE_NAME":"D17_R-23_2017-12-13.d"}
},
{
"Subject ID":"-",
"Sample ID":"D17_WHI-004_2018-03-16",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"8.82","RAW_FILE_NAME":"D17_WHI-004_2018-03-16.d"}
},
{
"Subject ID":"-",
"Sample ID":"D2D16_WHI-010_2018-04-23",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"11.72","RAW_FILE_NAME":"D2D16_WHI-010_2018-04-23.d"}
},
{
"Subject ID":"-",
"Sample ID":"G5_PS-A-67_25-06-2018",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"9.9","RAW_FILE_NAME":"G5_PS-A-67_25-06-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"G5_PS-R-28_20-06-2018",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"8.6","RAW_FILE_NAME":"G5_PS-R-28_20-06-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"G5_PS-WHI-103_30-04-2018",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"1.2","RAW_FILE_NAME":"G5_PS-WHI-103_30-04-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"G6_PS-R-25_11-01-2018",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.9","RAW_FILE_NAME":"G6_PS-R-25_11-01-2018.d"}
},
{
"Subject ID":"-",
"Sample ID":"MC-01_2017-07-05",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.08","RAW_FILE_NAME":"MC-01_2017-07-05.d"}
},
{
"Subject ID":"-",
"Sample ID":"MC-08_2017-09-14",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.23","RAW_FILE_NAME":"MC-08_2017-09-14.d"}
},
{
"Subject ID":"-",
"Sample ID":"R-11_2016-11-04",
"Factors":{"Time before death (weeks)":"3"},
"Additional sample data":{"Urine creatinine (mmol/L)":"2.68","RAW_FILE_NAME":"R-11_2016-11-04.d"}
},
{
"Subject ID":"-",
"Sample ID":"MC-04_2017-07-25",
"Factors":{"Time before death (weeks)":"4"},
"Additional sample data":{"Urine creatinine (mmol/L)":"3.13","RAW_FILE_NAME":"MC-04_2017-07-25.d"}
},
{
"Subject ID":"-",
"Sample ID":"A-02_2017-03-10",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"2.04","RAW_FILE_NAME":"A-02_2017-03-10.d"}
},
{
"Subject ID":"-",
"Sample ID":"A-16_2018-06-21",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"9.46","RAW_FILE_NAME":"A-16_2018-06-21.d"}
},
{
"Subject ID":"-",
"Sample ID":"A-17_2017-04-05",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"12.77","RAW_FILE_NAME":"A-17_2017-04-05.d"}
},
{
"Subject ID":"-",
"Sample ID":"A-43_2017-11-01",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"1.47","RAW_FILE_NAME":"A-43_2017-11-01.d"}
},
{
"Subject ID":"-",
"Sample ID":"A-58_2017-08-30",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.25","RAW_FILE_NAME":"A-58_2017-08-30.d"}
},
{
"Subject ID":"-",
"Sample ID":"R-06_2016-10-18",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"2.12","RAW_FILE_NAME":"R-06_2016-10-18.d"}
},
{
"Subject ID":"-",
"Sample ID":"R-14_2017-03-17",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"4.27","RAW_FILE_NAME":"R-14_2017-03-17.d"}
},
{
"Subject ID":"-",
"Sample ID":"R-16_2017-05-02",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"5.05","RAW_FILE_NAME":"R-16_2017-05-02.d"}
},
{
"Subject ID":"-",
"Sample ID":"R-19_2018-11-14",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"7.38","RAW_FILE_NAME":"R-19_2018-11-14.d"}
},
{
"Subject ID":"-",
"Sample ID":"R-31_2018-07-25",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"9.99","RAW_FILE_NAME":"R-31_2018-07-25.d"}
},
{
"Subject ID":"-",
"Sample ID":"WHI-006_2018-04-05",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"3.14","RAW_FILE_NAME":"WHI-006_2018-04-05.d"}
},
{
"Subject ID":"-",
"Sample ID":"WHI-100_2018-07-20",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"2.23","RAW_FILE_NAME":"WHI-100_2018-07-20.d"}
},
{
"Subject ID":"-",
"Sample ID":"WHI-105_2018-05-22",
"Factors":{"Time before death (weeks)":"4+"},
"Additional sample data":{"Urine creatinine (mmol/L)":"6.6","RAW_FILE_NAME":"WHI-105_2018-05-22.d"}
}
],
"COLLECTION":{"COLLECTION_SUMMARY":"The study was conducted at six sites (hospitals and hospices) in the North West of England (UK) from June 2016 to September 2018. Patients with lung cancer were recruited prospectively and multiple urine samples were collected up to three times a week while an inpatient. Ethical approval was provided by North Wales (West) Research Ethics Committee (REC reference 15/WA/0464). Research team members collected 20 mL of urine from participants in a universal container. For those participants with a urinary catheter, the urine was collected using a needle and syringe from the catheter port. The samples were stored on site in a locked freezer at −20°C. An anonymised record of the medication administered was collected. Collection protocol described previously by Coyle et al. (BMJ Open. 2016; 6(11) e011763. doi: 10.1136/bmjopen-2016-011763).","SAMPLE_TYPE":"Urine","VOLUMEORAMOUNT_COLLECTED":"20 mL","STORAGE_CONDITIONS":"-20℃"},

"TREATMENT":{"TREATMENT_SUMMARY":"Clinical observational study. Serial urine samples collected from patients with lung cancer in a palliative care setting at varying time points up until death; >12 weeks - 1 week before death (see 'study design' information). Although multiple samples were collected from patients, only the final sample was included in the analysis."},

"SAMPLEPREP":{"SAMPLEPREP_SUMMARY":"Individual patient samples were thawed at room temperature, vortexed and separated into four replicate aliquots in individual 96-well plates (Waters, UK) which were stored at -80 °C until analysis by one of four different methods; two different chromatography conditions in negative and positive ionisation polarity. Pooled quality control samples were created following the protocol described by Norman et al. (Clin Chem. 2019;65(4):530-39. doi: 10.1373/clinchem.2018.295345). For each sample group (time before death), a separate representative pool was created by pooling an equal volume of each individual urine sample for quality control purposes. An overall pool was also created by pooling equal proportions of the above group pools. Analysis of individual and pooled samples was performed following dilution of 1:3 urine:deionised water (DIRECT-Q 3UV Millipore water purification system) as previously described by Norman et al. (2019)."},

"CHROMATOGRAPHY":{"CHROMATOGRAPHY_SUMMARY":"LC method 1: employed an Atlantis dC18 column (3x100 mm, 3 µm, Waters, UK) maintained at 60 °C with flow rate at 0.4 mL/min. Mobile phases were (A) water and (B) methanol both containing 5 mmol/L ammonium formate and 0.1 % formic acid. The elution gradient started at 5 % B at 0 to 1 min increasing linearly to 100 % by 12 min, held at 100 % B until 14 min, returning to 95 % A for 5 min.","INSTRUMENT_NAME":"Agilent 6550","COLUMN_NAME":"Waters Atlantis dC18 (100 x 3mm,3um)","COLUMN_TEMPERATURE":"60","FLOW_GRADIENT":"The elution gradient started at 5 % B at 0 to 1 min increasing linearly to 100 % by 12 min, held at 100 % B until 14 min, returning to 95 % A for 5 min","FLOW_RATE":"0.4 mL/min","SOLVENT_A":"100% water; 0.1 % formic acid; 5 mM ammonium formate","SOLVENT_B":"100% methanol; 0.1 % formic acid; 5 mM ammonium formate","CHROMATOGRAPHY_TYPE":"Reversed phase"},

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

"MS":{"INSTRUMENT_NAME":"Agilent 6550 QTOF","INSTRUMENT_TYPE":"QTOF","MS_TYPE":"ESI","MS_COMMENTS":"Mass spectrometry conditions: The mass spectrometer was tuned and calibrated according to protocols recommended by the manufacturer. Acquisition was performed in 2 GHz mode and mass range 50-1700. The capillary voltage was 4000 V and fragmentor voltage 380 V. The desolvation gas temperature was 200 °C with flow rate at 15 L/min. The sheath gas temperature was 300 °C with flow rate at 12 L/min. The nebulizer pressure was 40 psig and nozzle voltage 1000 V (± for positive and negative ionisation modes). The acquisition rate was 3 spectra/second. The reference mass solution was continually infused at a flow rate of 0.5 mL/min by a separate isocratic pump for constant mass correction. Repeat injections of each pooled sample were interspersed throughout the analytical sequence, as per the quality control procedure described by Norman et al. (Clin Chem. 2019;65(4):530-539. doi: 10.1373/clinchem.2018.295345). The individual sample analysis order was randomised computationally. Data Pre-processing and Quality Control: All data were acquired using the MassHunter suite (Agilent build 6.0) with quality checks being performed by Qualitative Analysis (build 07.00). Mass accuracy was checked using extracted ion chromatograms of reference masses: the resulting accuracy was ±5 ppm during the run. Additionally, chromatographic reproducibility was checked by overlaying binary pump pressure curves across each analytical sequence. Data was filtered based upon the pooled QC samples, with compounds being retained if observed in 100 % of replicate injections for at least 1 pool and with peak area coefficient of variation (CV) <25 % across all replicate injections for each pool. A comprehensive semi-targeted approach was employed to assign the identity of urinary metabolites using an in-house compound library that included a broad range of metabolites involved in intermediary metabolism. Targeted feature extraction was performed on each dataset based on matching of metabolite chemical features against an accurate mass and retention time (AMRT) database previously generated from analysis of the IROA Technology MS metabolite library of tandards by each LC method described above, combined with the same QTOF analytical parameters used in this study (databases publicly available: https://doi.org/10.6084/m9.figshare.c.4378235.v2). In addition to accurate mass and retention time, MS/MS (data-dependent, employed for 'hit' metabolites) was also used in the confirmation of metabolite identity (i.e. level 1 identification) as per Sumner et al. Feature extraction was performed in MassHunter Profinder (build 10.0); accurate mass window of 10 ppm and retention time window of 0.3 min against the respective AMRT database. Data were exported in the format of a csv file for statistical analysis. Unidentified compounds are 'known unknowns' of interest from previous experiments; detection by matched AMRT and named in the format 'RT_neutral-mass'. 'BDRM'; unidentified bone-derived metabolite.","ION_MODE":"POSITIVE"},

"MS_METABOLITE_DATA":{
"Units":"Values are raw peak area",

"Data":[{"Metabolite":"10-hydroxy capric acid","D0D1_A-09_2017-11-21":"","D0D1_A-63_2018-03-28":"","D0D1_C-04_2017-08-10":"","D0D1_MC-05_2017-08-16":"","D0D1_R-26_2018-04-20":"","D0D1_R-29_2018-06-01":"45210.1220","D0D1_R-32_2018-07-13":"","D0D1_WHI-001_2018-03-14":"","D0D1_WHI-003_2018-04-16":"77811.6430","D0D1_WHI-011-106_2018-07-17":"278766.1536","D0D1_WHI-102_2018-04-25":"400990.5860","D2D16_A-57_2017-08-22":"133115.1405","D2D16_MC-11_2018-07-01":"","D2D16_WHI-015-107_2018-07-20":"","G1_PS-A-05_03-03-2017":"","G1_PS-A-51_21-11-2017":"50038.5694","G1_PS-MC-06_14-08-2017":"","G1_PS-R-02_11-10-2016":"","G1_PS-WHI-007_11-04-2018":"","G1_PS-WHI-020_15-06-2018":"37565.8229","G2_PS-MC-02_03-07-2017":"","G2_PS-R-09_01-11-2016":"","G2_PS-R-21_15-11-2017":"","G2_PS-WHI-027_04-09-2018":"","G3_PS-WHI-101_11-04-2018":"","A-01_2017-02-09":"","A-11_2018-05-17":"","A-12_2017-03-16":"","A-15_2018-06-06":"43833.1683","A-20_2017-11-21":"","A-21_2018-01-24":"30388.1247","A-24_2017-07-06":"","A-33_2017-12-12":"","A-40_2018-07-24":"","A-47_2017-08-02":"","A-48_2017-06-29":"","A-49_2017-06-28":"","A-61_2018-03-15":"","C-02_2017-03-16":"","C-03_2017-03-20":"","C-05_2017-04-20":"","C-06_2017-04-26":"","C-09_2017-05-10":"","C-13_2017-06-06":"","C-18_2017-06-21":"","D17_A-65_2018-07-07":"","LCC_PS-A-06_20-07-2017":"","LCC_PS-A-07_02-03-2017":"","LCC_PS-A-08_26-07-2017":"","LCC_PS-A-13_06-07-2017":"","LCC_PS-A-19_06-07-2017":"","LCC_PS-A-32_06-07-2017":"82428.1187","LCC_PS-A-50_29-06-2017":"","LCC_PS-C-01_09-03-2017":"","LCC_PS-C-12_01-06-2017":"","LCC_PS-MC-09_19-10-2017":"","LCC_PS-MC-14_27-02-2018":"","LCC_PS-R-15_31-03-2017":"","LCC_PS-R-22_08-12-2017":"","LCC_PS-R-24_11-01-2018":"","LCC_PS-WHI-002_14-03-2018":"","LCC_PS-WHI-008_16-04-2018":"","MC-15_2018-09-19":"","MC-16_2018-09-12":"","MC-17_2018-09-12":"","R-30_2018-06-07":"","WHI-016_2018-08-30":"52681.2670","D2D16_A-18_2017-04-04":"1110600.8320","D2D16_A-56_2017-08-23":"","D2D16_WHI-014_2018-06-05":"","D2D16_WHI-023_2018-08-29":"","D2D16_WHI-026_2018-07-19":"","G3_PS-A-14_26-06-2017":"","G3_PS-C-17_20-06-2017":"","G3_PS-R-12_02-03-2017":"209726.0660","G4_PS-A-62_15-02-2018":"","G4_PS-MC-10_06-03-2018":"","G4_PS-R-05_17-08-2016":"","G4_PS-R-17_14-06-2017":"945633.3191","G4_PS-WHI-012_01-05-2018":"","G5_PS-MC-07_14-08-2017":"37679.8659","G5_PS-MC-13_27-02-2018":"","G5_PS-R-01_15-06-2016":"","Group 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