#METABOLOMICS WORKBENCH maxmendez_20210921_063335_mwtab.txt DATATRACK_ID:2854 STUDY_ID:ST001925 ANALYSIS_ID:AN003128 PROJECT_ID:PR001215 VERSION 1 CREATED_ON September 21, 2021, 7:58 am #PROJECT PR:PROJECT_TITLE Metabolic Changes in Multiple Myeloma Patients after CFZ treatment PR:PROJECT_TYPE MS Untargeted Metabolomics from Human Serum PR:PROJECT_SUMMARY In this study we aimed to examine the acute metabolomic changes following PR:PROJECT_SUMMARY proteasome inhibition with Carfilzomib within 8h of treatment. PR:INSTITUTE University of Zurich PR:DEPARTMENT Department of Hematology-Oncology. Kantonsspital St. Gallen PR:LABORATORY Experimental Hematolgy-KSSG PR:LAST_NAME Mendez PR:FIRST_NAME Max PR:ADDRESS Rorschacherstrasse 95, 9007, St. Gallen. PR:EMAIL maxmendez@runbox.com PR:PHONE +41 71 494 10 67 #STUDY ST:STUDY_TITLE MS Untargeted Metabolomics from Human Serum ST:STUDY_SUMMARY Multiple Myeloma patients were treated with the proteasome inhibitor carfilzomib ST:STUDY_SUMMARY in different protocols according to their clinical stage. Paired serum samples ST:STUDY_SUMMARY were obtained before i.v injection and after 1-8h post treatment and snap ST:STUDY_SUMMARY frozen. Samples were stored at -80°C until analysis. ST:INSTITUTE University of Zurich ST:LAST_NAME Mendez ST:FIRST_NAME Max ST:ADDRESS Rorschacherstrasse 95. 9007, St.Gallen ST:EMAIL maxmendez@runbox.com ST:PHONE +41 71 494 10 67 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 6 ST:NUM_MALES 5 ST:NUM_FEMALES 1 #SUBJECT SU:SUBJECT_TYPE Human SU:SUBJECT_SPECIES Homo sapiens SU:TAXONOMY_ID 9606 SU:AGE_OR_AGE_RANGE 49-79 years old SU:GENDER Male and female SU:HUMAN_MEDICATIONS All patients had received at lest 3 lines of anti-myeloma therapy #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Raw file names and additional sample data SUBJECT_SAMPLE_FACTORS - QC_06_NEG class:QC RAW_FILE_NAME=20200721_QC_06_NEG; order=1 SUBJECT_SAMPLE_FACTORS - QC_07_NEG class:QC RAW_FILE_NAME=20200721_QC_07_NEG; order=2 SUBJECT_SAMPLE_FACTORS - QC_08_NEG class:QC RAW_FILE_NAME=20200721_QC_08_NEG; order=3 SUBJECT_SAMPLE_FACTORS - QC_09_NEG class:QC RAW_FILE_NAME=20200721_QC_09_NEG; order=4 SUBJECT_SAMPLE_FACTORS - QC_10_NEG class:QC RAW_FILE_NAME=20200721_QC_10_NEG; order=5 SUBJECT_SAMPLE_FACTORS - Pre1_NEG class:PRETREATMENT RAW_FILE_NAME=20P04890001_NEG; order=6 SUBJECT_SAMPLE_FACTORS - Post2_NEG class:POSTREATMENT RAW_FILE_NAME=20P04890011_NEG; order=8 SUBJECT_SAMPLE_FACTORS - Post4_NEG class:POSTREATMENT RAW_FILE_NAME=20P04890014_NEG; order=9 SUBJECT_SAMPLE_FACTORS - Post6_NEG class:POSTREATMENT RAW_FILE_NAME=20P04890016_NEG; order=10 SUBJECT_SAMPLE_FACTORS - Pre2_NEG class:PRETREATMENT RAW_FILE_NAME=20P04890002_NEG; order=11 SUBJECT_SAMPLE_FACTORS - Pre3_NEG class:PRETREATMENT RAW_FILE_NAME=20P04890003_NEG; order=12 SUBJECT_SAMPLE_FACTORS - Post1_NEG class:POSTREATMENT RAW_FILE_NAME=20P04890010_NEG; order=13 SUBJECT_SAMPLE_FACTORS - Post5_NEG class:POSTREATMENT RAW_FILE_NAME=20P04890015_NEG; order=14 SUBJECT_SAMPLE_FACTORS - Pre4_NEG class:PRETREATMENT RAW_FILE_NAME=20P04890004_NEG; order=15 SUBJECT_SAMPLE_FACTORS - QC_11_NEG class:QC RAW_FILE_NAME=20200721_QC_11_NEG; order=16 SUBJECT_SAMPLE_FACTORS - Pre5_NEG class:PRETREATMENT RAW_FILE_NAME=20P04890005_NEG; order=18 SUBJECT_SAMPLE_FACTORS - Post3_NEG class:POSTREATMENT RAW_FILE_NAME=20P04890012_NEG; order=19 SUBJECT_SAMPLE_FACTORS - Pre6_NEG class:PRETREATMENT RAW_FILE_NAME=20P04890006_NEG; order=20 SUBJECT_SAMPLE_FACTORS - QC_12_NEG class:QC RAW_FILE_NAME=20200721_QC_12_NEG; order=22 SUBJECT_SAMPLE_FACTORS - QC_13_NEG class:QC RAW_FILE_NAME=20200721_QC_13_NEG; order=23 SUBJECT_SAMPLE_FACTORS - QC_14_NEG class:QC RAW_FILE_NAME=20200721_QC_14_NEG; order=24 SUBJECT_SAMPLE_FACTORS - QC_06_POS class:QC RAW_FILE_NAME=20200721_QC_06_POS; order=1 SUBJECT_SAMPLE_FACTORS - QC_07_POS class:QC RAW_FILE_NAME=20200721_QC_07_POS; order=2 SUBJECT_SAMPLE_FACTORS - QC_08_POS class:QC RAW_FILE_NAME=20200721_QC_08_POS; order=3 SUBJECT_SAMPLE_FACTORS - QC_09_POS class:QC RAW_FILE_NAME=20200721_QC_09_POS; order=4 SUBJECT_SAMPLE_FACTORS - QC_10_POS class:QC RAW_FILE_NAME=20200721_QC_10_POS; order=5 SUBJECT_SAMPLE_FACTORS - Pre1_POS class:PRETREATMENT RAW_FILE_NAME=20P04890001_POS; order=6 SUBJECT_SAMPLE_FACTORS - Post2_POS class:POSTREATMENT RAW_FILE_NAME=20P04890011_POS; order=8 SUBJECT_SAMPLE_FACTORS - Post4_POS class:POSTREATMENT RAW_FILE_NAME=20P04890014_POS; order=9 SUBJECT_SAMPLE_FACTORS - Post6_POS class:POSTREATMENT RAW_FILE_NAME=20P04890016_POS; order=10 SUBJECT_SAMPLE_FACTORS - Pre2_POS class:PRETREATMENT RAW_FILE_NAME=20P04890002_POS; order=11 SUBJECT_SAMPLE_FACTORS - Pre3_POS class:PRETREATMENT RAW_FILE_NAME=20P04890003_POS; order=12 SUBJECT_SAMPLE_FACTORS - Post1_POS class:POSTREATMENT RAW_FILE_NAME=20P04890010_POS; order=13 SUBJECT_SAMPLE_FACTORS - Post5_POS class:POSTREATMENT RAW_FILE_NAME=20P04890015_POS; order=14 SUBJECT_SAMPLE_FACTORS - Pre4_POS class:PRETREATMENT RAW_FILE_NAME=20P04890004_POS; order=15 SUBJECT_SAMPLE_FACTORS - QC_11_POS class:QC RAW_FILE_NAME=20200721_QC_11_POS; order=16 SUBJECT_SAMPLE_FACTORS - Pre5_POS class:PRETREATMENT RAW_FILE_NAME=20P04890005_POS; order=18 SUBJECT_SAMPLE_FACTORS - Post3_POS class:POSTREATMENT RAW_FILE_NAME=20P04890012_POS; order=19 SUBJECT_SAMPLE_FACTORS - Pre6_POS class:PRETREATMENT RAW_FILE_NAME=20P04890006_POS; order=20 SUBJECT_SAMPLE_FACTORS - QC_12_POS class:QC RAW_FILE_NAME=20200721_QC_12_POS; order=22 SUBJECT_SAMPLE_FACTORS - QC_13_POS class:QC RAW_FILE_NAME=20200721_QC_13_POS; order=23 SUBJECT_SAMPLE_FACTORS - QC_14_POS class:QC RAW_FILE_NAME=20200721_QC_14_POS; order=24 #COLLECTION CO:COLLECTION_SUMMARY Anesthesia was induced with Ketamine 80 mg/kg intramuscular and maintained with CO:COLLECTION_SUMMARY Isoflurane 0.5%. Plasma was obtained by centrifugation after cervical CO:COLLECTION_SUMMARY dislocation under anesthesia. Samples were snap frozen in dry ice and kept at CO:COLLECTION_SUMMARY -80°C until analysis. CO:SAMPLE_TYPE Blood (plasma) CO:STORAGE_CONDITIONS Described in summary #TREATMENT TR:TREATMENT_SUMMARY See attached file TR:TREATMENT_COMPOUND Carfilzomib i.v TR:TREATMENT_ROUTE i.v TR:TREATMENT_DOSE As described in attached file #SAMPLEPREP SP:SAMPLEPREP_SUMMARY No. Step 1 Take 40 μL of each sample into the 96-well plate; 2 Insert fetal SP:SAMPLEPREP_SUMMARY bovine serum (more than 50, insert one for every 10 samples; 50 or less are not SP:SAMPLEPREP_SUMMARY considered); 3 Add 120 μL of pre-cooled methanol, mix and shake for 1 min, and SP:SAMPLEPREP_SUMMARY place in a refrigerator at -20°C for 2h or overnight; 4 4,000g * 4°C SP:SAMPLEPREP_SUMMARY centrifugation for 30 min; 5 Place 25 μL of each sample in a new 96-well plate SP:SAMPLEPREP_SUMMARY and dilute with 225 μL of 50% methanol; 6 Take 50 μL of each sample and mix to SP:SAMPLEPREP_SUMMARY QC sample; 7 Take 60 μL of the supernatant and transfer to a 96-well SP:SAMPLEPREP_SUMMARY microplate, seal the membrane and test it on the machine. SP:PROCESSING_STORAGE_CONDITIONS -80℃ SP:EXTRACT_STORAGE -80℃ #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY All samples were acquired by the LC-MS system followed machine orders. Firstly, CH:CHROMATOGRAPHY_SUMMARY all chromatographic separations were performed using an ultra performance liquid CH:CHROMATOGRAPHY_SUMMARY chromatography (UPLC) system (Waters, UK). An ACQUITY UPLC HSS T3 column (100 CH:CHROMATOGRAPHY_SUMMARY mm*2.1 mm, 1.8 μm, Waters, UK) was used for the reversed phase separation. The CH:CHROMATOGRAPHY_SUMMARY column oven was maintained at 50 °C. The flow rate was 0.4 ml/min and the CH:CHROMATOGRAPHY_SUMMARY mobile phase consisted of solvent A (water + 0.1% formic acid) and solvent B CH:CHROMATOGRAPHY_SUMMARY (methanol + 0.1% formic acid). Gradient elution conditions were set as follows: CH:CHROMATOGRAPHY_SUMMARY 0~2 min, 100% phase A; 2~11 min, 0% to 100% B; 11~13 min, 100% B; 13~15 min, 0% CH:CHROMATOGRAPHY_SUMMARY to 100% A. The injection volume for each sample was 5 µL. CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME Waters Acquity CH:COLUMN_NAME Waters Acquity BEH HSS T3 (100 x 2.1mm, 1.8um) CH:FLOW_GRADIENT 0.4 ml/min CH:SOLVENT_A water + 0.1% formic acid CH:SOLVENT_B methanol + 0.1% formic acid #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Waters Xevo-TQ MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS he additive ions when the substance is ionized at the ion source are negative MS:MS_COMMENTS ions such as COOH-, OH-. , the capillary and sampling cone voltages were set at MS:MS_COMMENTS 2.0 kV and 40.0 V, respectively. MS:MS_RESULTS_FILE ST001925_AN003128_Results.txt UNITS:m/z Has m/z:Yes Has RT:Yes RT units:Minutes #END