#METABOLOMICS WORKBENCH plyush1993_20191029_070718 DATATRACK_ID:1841 STUDY_ID:ST001271 ANALYSIS_ID:AN002111 VERSION 1 CREATED_ON 05-02-2023 #PROJECT PR:PROJECT_TITLE Colorectal cancer before and after surgery metabolomics data integration PR:PROJECT_TYPE Pilot study PR:PROJECT_SUMMARY In this study 40 urine samples were analyzed in 5 batches. There are 3 labels: PR:PROJECT_SUMMARY control group volunteers (8 pcs., CG), colorectal cancer patients before PR:PROJECT_SUMMARY surgical operation (20 pcs., pre) and after surgical operation (12 pcs., post). PR:INSTITUTE Lomonosov Moscow State University PR:DEPARTMENT Chemistry PR:LABORATORY Mass spectrometry PR:LAST_NAME Plyushchenko PR:FIRST_NAME Ivan PR:ADDRESS Leninskie gory, 1/3, Moscow, Moscow, 119234, Russian Federation PR:EMAIL plyush1993@bk.ru PR:PHONE +79160362200 PR:PUBLICATIONS Plyushchenko Ivan, et al. "An approach for feature selection with data modelling PR:PUBLICATIONS in LC-MS metabolomics." Analytical Methods 12.28 (2020): 3582-3591. DOI: PR:PUBLICATIONS 10.1039/d0ay00204f PR:DOI http://dx.doi.org/10.21228/M8X110 PR:CONTRIBUTORS Rodin I., Shakhmatov D., Bolotnik T. #STUDY ST:STUDY_TITLE Colorectal cancer before and after surgery metabolomics data integration ST:STUDY_TYPE Pilot study ST:STUDY_SUMMARY In this study 40 urine samples were analyzed in 5 batches. There are 3 labels: ST:STUDY_SUMMARY control group volunteers (8 pcs., CG), colorectal cancer patients before ST:STUDY_SUMMARY surgical operation (20 pcs., pre) and after surgical operation (12 pcs., post). ST:INSTITUTE Lomonosov MSU ST:DEPARTMENT Chemistry ST:LABORATORY Mass spectrometry ST:LAST_NAME Plyushchenko ST:FIRST_NAME Ivan ST:ADDRESS Leninskie gory, 1/3 ST:EMAIL plyush1993@bk.ru ST:PHONE 89160362200 ST:SUBMIT_DATE 2019-10-29 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - 22CG Treatment:CG Order=33; Batch=5 SUBJECT_SAMPLE_FACTORS - 23CG Treatment:CG Order=34; Batch=5 SUBJECT_SAMPLE_FACTORS - 24CG Treatment:CG Order=35; Batch=5 SUBJECT_SAMPLE_FACTORS - 25CG Treatment:CG Order=36; Batch=5 SUBJECT_SAMPLE_FACTORS - 26CG Treatment:CG Order=37; Batch=5 SUBJECT_SAMPLE_FACTORS - 27CG Treatment:CG Order=38; Batch=5 SUBJECT_SAMPLE_FACTORS - 28CG Treatment:CG Order=39; Batch=5 SUBJECT_SAMPLE_FACTORS - 29CG Treatment:CG Order=40; Batch=5 SUBJECT_SAMPLE_FACTORS - 10post Treatment:post Order=16; Batch=2 SUBJECT_SAMPLE_FACTORS - 11post Treatment:post Order=23; Batch=4 SUBJECT_SAMPLE_FACTORS - 18post Treatment:post Order=26; Batch=4 SUBJECT_SAMPLE_FACTORS - 19post Treatment:post Order=28; Batch=4 SUBJECT_SAMPLE_FACTORS - 1post Treatment:post Order=2; Batch=1 SUBJECT_SAMPLE_FACTORS - 20post Treatment:post Order=30; Batch=4 SUBJECT_SAMPLE_FACTORS - 21post Treatment:post Order=32; Batch=4 SUBJECT_SAMPLE_FACTORS - 2post Treatment:post Order=4; Batch=1 SUBJECT_SAMPLE_FACTORS - 3post Treatment:post Order=6; Batch=1 SUBJECT_SAMPLE_FACTORS - 4post Treatment:post Order=8; Batch=1 SUBJECT_SAMPLE_FACTORS - 5post Treatment:post Order=10; Batch=1 SUBJECT_SAMPLE_FACTORS - 6post Treatment:post Order=12; Batch=1 SUBJECT_SAMPLE_FACTORS - 11pre Treatment:pre Order=17; Batch=2 SUBJECT_SAMPLE_FACTORS - 12pre Treatment:pre Order=18; Batch=3 SUBJECT_SAMPLE_FACTORS - 13pre Treatment:pre Order=19; Batch=3 SUBJECT_SAMPLE_FACTORS - 14pre Treatment:pre Order=20; Batch=3 SUBJECT_SAMPLE_FACTORS - 15pre Treatment:pre Order=21; Batch=3 SUBJECT_SAMPLE_FACTORS - 16pre Treatment:pre Order=22; Batch=3 SUBJECT_SAMPLE_FACTORS - 17pre Treatment:pre Order=24; Batch=4 SUBJECT_SAMPLE_FACTORS - 18pre Treatment:pre Order=25; Batch=4 SUBJECT_SAMPLE_FACTORS - 19pre Treatment:pre Order=27; Batch=4 SUBJECT_SAMPLE_FACTORS - 1pre Treatment:pre Order=1; Batch=1 SUBJECT_SAMPLE_FACTORS - 20pre Treatment:pre Order=29; Batch=4 SUBJECT_SAMPLE_FACTORS - 21pre Treatment:pre Order=31; Batch=4 SUBJECT_SAMPLE_FACTORS - 2pre Treatment:pre Order=3; Batch=1 SUBJECT_SAMPLE_FACTORS - 3pre Treatment:pre Order=5; Batch=1 SUBJECT_SAMPLE_FACTORS - 4pre Treatment:pre Order=7; Batch=1 SUBJECT_SAMPLE_FACTORS - 5pre Treatment:pre Order=9; Batch=1 SUBJECT_SAMPLE_FACTORS - 6pre Treatment:pre Order=11; Batch=1 SUBJECT_SAMPLE_FACTORS - 7pre Treatment:pre Order=13; Batch=2 SUBJECT_SAMPLE_FACTORS - 8pre Treatment:pre Order=14; Batch=2 SUBJECT_SAMPLE_FACTORS - 9pre Treatment:pre Order=15; Batch=2 #COLLECTION CO:COLLECTION_SUMMARY 40 urine samples were analyzed in 5 batches. There are 3 labels: control group CO:COLLECTION_SUMMARY volunteers (8 pcs., CG), colorectal cancer patients before surgical operation CO:COLLECTION_SUMMARY (20 pcs., pre) and after surgical operation (12 pcs., post). CO:SAMPLE_TYPE Urine CO:STORAGE_CONDITIONS -20℃ #TREATMENT TR:TREATMENT_SUMMARY All morning fasting urine samples (on an empty stomach, immediately after sleep) TR:TREATMENT_SUMMARY from the State Scientific Center of Coloproctology (Moscow, Russia) were TR:TREATMENT_SUMMARY collected in sterilized plastic sealed falcons for this study and were frozen in TR:TREATMENT_SUMMARY the refrigerator at -20 °C. Then the samples in containers with cold cells were TR:TREATMENT_SUMMARY transported to the laboratory. In control group patients with fistula, TR:TREATMENT_SUMMARY hemorrhoid, diverticulosis, irritable bowel syndrome and anal fissure were TR:TREATMENT_SUMMARY included. In the sample group after the operation, samples were collected no TR:TREATMENT_SUMMARY more than three days after the operation. In the sample group before the TR:TREATMENT_SUMMARY operation, patients with different histological stages (G1-G3) were involved. TR:TREATMENT_SUMMARY The age and sex of the collected subjects were matched as much as possible. All TR:TREATMENT_SUMMARY the samples were stored at -24 ˚C until analysis and were defrosted at room TR:TREATMENT_SUMMARY temperature prior the analysis. #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Prior to analysis, samples were defrosted at room temperature and centrifuged at SP:SAMPLEPREP_SUMMARY 16000 rpm for 15 min, then aliquots of the supernatant were diluted in 5-fold by SP:SAMPLEPREP_SUMMARY deionized water with a final papaverine concentration of 0.2 µg mL-1 and SP:SAMPLEPREP_SUMMARY centrifuged at 16000 rpm for 15 min and then aliquots of supernatant were placed SP:SAMPLEPREP_SUMMARY into vials. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Two solvents were used: (A) deionized water with 0,1% formic acid, and (B) MeCN. CH:CHROMATOGRAPHY_SUMMARY After a 5 min hold at 5.0% solvent B, elution was performed according to the CH:CHROMATOGRAPHY_SUMMARY following conditions: from 5.0% B to 59% B in 30 min; to 95% B in 7 min; keeping CH:CHROMATOGRAPHY_SUMMARY constant for 10 min, to 5% B in 3 min, followed by 5 min of equilibration on the CH:CHROMATOGRAPHY_SUMMARY initial conditions. The flow rate was 0.3 mL•min-1. The injection volume was 5 CH:CHROMATOGRAPHY_SUMMARY μL. CH:CHROMATOGRAPHY_COMMENTS Acquity UPLC BEH; 1.7 μm 2.1 × 5 mm UHPLC Guard 3PK Zorbax SB-C18 1.8 μm CH:CHROMATOGRAPHY_COMMENTS guard column CH:INSTRUMENT_NAME Shimadzu 20AD CH:COLUMN_NAME ACQUITY UPLC BEH C18 (1.7 µm, 2.1 mm X 5 mm);Agilent ZORBAX StableBond C18 CH:COLUMN_NAME UHPLC guard (4.6 mm, 1.8 µm) CH:COLUMN_PRESSURE 300-500 bar CH:COLUMN_TEMPERATURE 30 CH:FLOW_GRADIENT non-linear CH:FLOW_RATE 0.3 ml/min CH:INJECTION_TEMPERATURE 5 CH:INTERNAL_STANDARD papaverine CH:SOLVENT_A 100% water; 0.1% formic acid CH:SOLVENT_B 100% acetonitrile CH:CHROMATOGRAPHY_TYPE Reversed phase #ANALYSIS AN:ANALYSIS_TYPE MS AN:SOFTWARE_VERSION LabSolution 3.80.410 AN:DATA_FORMAT .lcd #MS MS:INSTRUMENT_NAME Shimadzu LCMS-IT-TOF MS:INSTRUMENT_TYPE Other MS:MS_TYPE ESI MS:MS_COMMENTS Mass range: 100 – 850 Da (SCAN mode). Other MS parameters were default MS:MS_COMMENTS (manufacturer recommendations). MS:ION_MODE POSITIVE MS:CAPILLARY_VOLTAGE 1.55 kV MS:DRY_GAS_FLOW 100 kPa MS:SOURCE_TEMPERATURE 200 MS:CDL_TEMPERATURE 200 MS:INTERFACE_VOLTAGE 4.5 kV MS:MS_RESULTS_FILE ST001271_AN002111_Results.txt UNITS:Area Has m/z:Yes Has RT:Yes RT units:Minutes #END