#METABOLOMICS WORKBENCH jikang_20220615_034018_mwtab.txt DATATRACK_ID:3305 STUDY_ID:ST002197 ANALYSIS_ID:AN003596 PROJECT_ID:PR001400 VERSION 1 CREATED_ON June 15, 2022, 6:28 pm #PROJECT PR:PROJECT_TITLE Myositis metabolomics PR:PROJECT_TYPE MS quantitative analysis PR:PROJECT_SUMMARY Targeted metabolomics study for C-protein induced myositis mouse model PR:INSTITUTE Seoul national university PR:LAST_NAME Kang PR:FIRST_NAME Jihyun PR:ADDRESS 502ho Intergrative Biomedical Education Research Building, 101 Deahakro, PR:ADDRESS Jongro-gu, Seoul, 03080, Korea, South PR:EMAIL jikang@snu.ac.kr PR:PHONE +821071014069 #STUDY ST:STUDY_TITLE Metabolic signature of C-protein induced myositis mouse model ST:STUDY_SUMMARY Objective of this study was to find Metabolic signature of C-protein induced ST:STUDY_SUMMARY myositis mouse model. We used the tissue samples of C-protein induced myositis ST:STUDY_SUMMARY mouse model and control using biocrates p180 kit. ST:INSTITUTE Seoul National University ST:LAST_NAME Kang ST:FIRST_NAME Jihyun ST:ADDRESS 502ho Intergrative Biomedical Education Research Building, 101 Deahakro, ST:ADDRESS Jongro-gu, Seoul, 03080, Korea, South Korea ST:EMAIL jikang@snu.ac.kr ST:PHONE +821071014069 #SUBJECT SU:SUBJECT_TYPE Mammal SU:SUBJECT_SPECIES Mus musculus #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 - 1 Factor:Control RAW_FILE_NAME=KIT2-0-5404_1036508975_50_0_1_1_00_1036509698.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_50_0_1_1_00_1036509698.wiff SUBJECT_SAMPLE_FACTORS - 2 Factor:Control RAW_FILE_NAME=KIT2-0-5404_1036508975_62_0_1_1_00_1036509709.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_62_0_1_1_00_1036509709.wiff SUBJECT_SAMPLE_FACTORS - 3 Factor:Control RAW_FILE_NAME=KIT2-0-5404_1036508975_74_0_1_1_00_1036509713.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_74_0_1_1_00_1036509713.wiff SUBJECT_SAMPLE_FACTORS - 10 Factor:Control RAW_FILE_NAME=KIT2-0-5404_1036508975_63_0_1_1_00_1036509785.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_63_0_1_1_00_1036509785.wiff SUBJECT_SAMPLE_FACTORS - 11 Factor:Control RAW_FILE_NAME=KIT2-0-5404_1036508975_75_0_1_1_00_1036509790.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_75_0_1_1_00_1036509790.wiff SUBJECT_SAMPLE_FACTORS - 12 Factor:Control RAW_FILE_NAME=KIT2-0-5404_1036508975_87_0_1_1_00_1036509801.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_87_0_1_1_00_1036509801.wiff SUBJECT_SAMPLE_FACTORS - 13 Factor:Control RAW_FILE_NAME=KIT2-0-5404_1036508975_04_0_1_1_00_1036509815.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_04_0_1_1_00_1036509815.wiff SUBJECT_SAMPLE_FACTORS - 14 Factor:Control RAW_FILE_NAME=KIT2-0-5404_1036508975_16_0_1_1_00_1036509820.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_16_0_1_1_00_1036509820.wiff SUBJECT_SAMPLE_FACTORS - 4 Factor:CIM RAW_FILE_NAME=KIT2-0-5404_1036508975_86_0_1_1_00_1036509728.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_86_0_1_1_00_1036509728.wiff SUBJECT_SAMPLE_FACTORS - 5 Factor:CIM RAW_FILE_NAME=KIT2-0-5404_1036508975_03_0_1_1_00_1036509732.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_03_0_1_1_00_1036509732.wiff SUBJECT_SAMPLE_FACTORS - 6 Factor:CIM RAW_FILE_NAME=KIT2-0-5404_1036508975_15_0_1_1_00_1036509747.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_15_0_1_1_00_1036509747.wiff SUBJECT_SAMPLE_FACTORS - 15 Factor:CIM RAW_FILE_NAME=KIT2-0-5404_1036508975_28_0_1_1_00_1036509834.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_28_0_1_1_00_1036509834.wiff SUBJECT_SAMPLE_FACTORS - 17 Factor:CIM RAW_FILE_NAME=KIT2-0-5404_1036508975_52_0_1_1_00_1036509853.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_52_0_1_1_00_1036509853.wiff SUBJECT_SAMPLE_FACTORS - 18 Factor:CIM RAW_FILE_NAME=KIT2-0-5404_1036508975_64_0_1_1_00_1036509868.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_64_0_1_1_00_1036509868.wiff SUBJECT_SAMPLE_FACTORS - 19 Factor:CIM RAW_FILE_NAME=KIT2-0-5404_1036508975_76_0_1_1_00_1036509872.wiff; RAW_FILE_NAME=KIT3-0-5505_1036508980_76_0_1_1_00_1036509872.wiff #COLLECTION CO:COLLECTION_SUMMARY tissue was collected in Seoul national university . CO:SAMPLE_TYPE muscle tissue #TREATMENT TR:TREATMENT_SUMMARY N/A #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Centrifuge the calibration standards, QC, and ISTD mix vials before opening at SP:SAMPLEPREP_SUMMARY 10 000 x g (rcf) for 2 min. Dissolve calibration standards (red caps) in 100 SP:SAMPLEPREP_SUMMARY µL water. Dissolve QCs (green, blue and yellow caps) in 100 µL water. SP:SAMPLEPREP_SUMMARY Dissolve ISTD mix (orange cap) in 1200 µL water. Shake all vials (Cal, QCs, SP:SAMPLEPREP_SUMMARY ISTD) for 15 min at 1200 rpm and vortex several times. Centrifuge the QCs SP:SAMPLEPREP_SUMMARY and your plasma samples for 5 min at 2750 x g (rcf) and 4 °C. Add 10 µL of SP:SAMPLEPREP_SUMMARY the ISTD mix to each well of the Kit plate except A1. Pipette 10 µL PBS / Cal / SP:SAMPLEPREP_SUMMARY QC / sample according to your plate layout generated by MetIDQTM. Dry for 30 SP:SAMPLEPREP_SUMMARY min under nitrogen (using a Nitrogen Evaporator or a Pressure Manifold). SP:SAMPLEPREP_SUMMARY Prepare the pre-mix for derivatization in the plastic tube of the Kit box (1900 SP:SAMPLEPREP_SUMMARY µL of each: ethanol, water and pyridine). Add 300 µL phenylisothiocyanate SP:SAMPLEPREP_SUMMARY (PITC) and vortex rigorously (at least 10 sec) until the derivatization solution SP:SAMPLEPREP_SUMMARY is clear. Make half of the solution for the starter kit. Add 50 µL of the SP:SAMPLEPREP_SUMMARY derivatization solution to each well using a repeater at maximum dispensing SP:SAMPLEPREP_SUMMARY speed. Cover the plate with the plastic lid and incubate for 25 min, then SP:SAMPLEPREP_SUMMARY dry for 60 min under nitrogen. Prepare extraction solvent and add 300 µL to SP:SAMPLEPREP_SUMMARY each well. You can use the repeater at low dispensing speed or an 8-channel SP:SAMPLEPREP_SUMMARY pipette. Shake for 30 min at 450 rpm (on the scale of min-max 0-1400 rpm). SP:SAMPLEPREP_SUMMARY Centrifuge for 2 min at 500 x g (rcf) or use a Pressure Manifold. Visually check SP:SAMPLEPREP_SUMMARY that the fill level is the same in all wells of the capture plate. If not, SP:SAMPLEPREP_SUMMARY repeat and apply higher g or higher pressure, respectively. Carefully remove the SP:SAMPLEPREP_SUMMARY upper filter plate and transfer the volume specified for your instrument to SP:SAMPLEPREP_SUMMARY another empty 96-deep well plate that you find in the Kit box (label “LC SP:SAMPLEPREP_SUMMARY plate”). Use an 8-channel pipette. Finish the LC plate and dilute the extracts SP:SAMPLEPREP_SUMMARY as described for your instrument Prepare the FIA plate and dilute the original SP:SAMPLEPREP_SUMMARY extracts as described for your instrument Seal both plates with the silicon mat. SP:SAMPLEPREP_SUMMARY Firmly press the mat’s naps into the wells. Shake both plates for 2 min at SP:SAMPLEPREP_SUMMARY 600 rpm. Put the plates in the autosampler. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE Reversed phase CH:INSTRUMENT_NAME AB SCIEX QTRAP 5500 CH:COLUMN_NAME Waters ACQUITY UPLC® BEH C18 1.7 µm 2.1 x 75 mm (No. 186005604) #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME ABI Sciex 5500 QTrap MS:INSTRUMENT_TYPE QTRAP MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS - #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS ng/mL MS_METABOLITE_DATA_START Samples 4 5 6 15 17 18 19 1 2 3 10 11 12 13 14 Factors Factor:CIM Factor:CIM Factor:CIM Factor:CIM Factor:CIM Factor:CIM Factor:CIM Factor:Control Factor:Control Factor:Control Factor:Control Factor:Control Factor:Control Factor:Control Factor:Control Asp 89.3 67.6 48.8 82.7 53.4 49.6 104 196 364 93.9 182 267 53.3 189 189 His 72 49.6 32.8 56.1 46.5 43.2 64.1 99.3 104 59.2 67.7 89 47 84.5 95.7 Met 70.7 45 28.5 49.9 58.7 62.7 65.5 81.4 91.2 84.1 91.3 73.3 45.5 69.2 80.9 Thr 139 83.7 73 133 143 104 127 193 182 123 195 198 106 162 173 Tyr 72.4 53.2 36.9 76.9 75.8 74.8 81.3 94.2 113 78.1 93.3 93 55.6 98.6 92.5 Carnosine 68.9 61 35.6 122 105 98.4 140 222 194 217 157 192 117 215 177 Creatinine 59.4 40.1 18.8 43.7 43.1 43.3 63.7 83 102 71 67.6 85.9 62 100 81.3 Spermidine 2.25 2.03 0.507 4.09 2.63 2.66 3.75 6.14 7.81 4.35 4.21 5.76 1.76 6.5 3.99 Spermine 0.99 0.94 0.198 1.15 0.624 0.492 1.55 2.41 3.94 1.58 0.899 4.15 0.945 4.2 2.27 Taurine 424.35 435.746 456.771 425.07 430.224 429.967 421.424 383.285 392.273 429.831 423.524 398.748 419.73 414.534 404.844 C0 52.1 39.9 20.5 41.2 58.6 45.6 64.2 99.5 127 83.7 69.4 84.9 49.2 75.5 86.9 C2 14.8 12.7 8.99 19.3 17.2 9.31 17.9 24.3 20.1 15.8 13.1 34.3 18.1 27.1 25.4 C14:1 0.074 0.065 0.065 0.011 0.011 0.011 0.055 0.011 0.163 0.07 0.079 0.109 0.069 0.085 0.082 C16:1 0.2 0.135 0.036 0.031 0.054 0.08 0.057 0.188 0.406 0.182 0.159 0.245 0.192 0.163 0.221 C16:1-OH 0.023 0.017 0.02 0.018 0.0034 0.0034 0.019 0.018 0.027 0.021 0.02 0.026 0.034 0.032 0.02 C18:1 2.15 1.47 0.466 0.768 0.88 0.959 1.1 2.55 4.02 1.99 1.76 2.38 2.21 1.55 1.94 C18:1-OH 0.029 0.024 0.019 0.022 0.02 0.027 0.02 0.026 0.034 0.034 0.03 0.035 0.042 0.057 0.028 C18:2 0.59 0.307 0.111 0.111 0.343 0.215 0.268 1.5 2.11 0.467 0.313 0.82 0.526 0.422 1 PC aa C30:2 0.047 0.038 0.038 0.042 0.052 0.038 0.044 0.021 0.016 0.038 0.03 0.015 0.044 0.016 0.033 PC aa C32:0 25.9 38.7 38.5 20.9 23.3 21.6 11.3 5.4 3.05 15.4 14 3.06 19.4 3.72 7.22 PC aa C32:1 33.9 41.7 36.3 27.5 38.9 34.9 25.3 7.46 4.53 29.4 27.2 5.47 26.7 5.71 12.8 PC aa C32:2 8.03 8.27 6.22 6.51 9.49 7.32 6.51 1.87 1.1 5.02 4.92 1.28 5.08 1.43 2.6 PC aa C34:1 89.3 128 137 82.6 113 121 61.2 19.9 12.2 68.1 74.3 11.8 80 23.5 32.2 PC aa C34:2 138 196 210 157 188 197 154 39.1 25.1 110 145 26.2 115 64.9 56.2 PC aa C34:3 16.1 16.6 12.9 13.9 21.5 17.8 13.5 3.15 1.93 9.31 11.3 2.23 10.3 3.05 4.58 PC aa C36:0 7.36 9.13 7.41 6.45 11.4 10.6 3.53 1.92 0.94 3.97 6.38 0.877 6.91 1.27 2.22 PC aa C36:1 7.73 12.3 15.4 7.07 8.52 10.3 3.73 1.41 0.876 3.78 4.12 0.524 5.75 3.51 1.39 PC aa C36:2 46.2 66.8 67.5 39.1 58 58.1 28.4 6.72 5.06 18.4 24.4 2.87 26.6 28.9 6.87 PC aa C36:3 51.2 64 52 46 63.9 66.7 35.4 9.71 5.54 30.8 41.9 5.25 44.5 12.3 12.3 PC aa C38:0 0.989 1.35 1.22 1.17 1.32 1.36 0.582 0.323 0.0646 0.618 0.859 0.0646 1.03 0.359 0.379 PC aa C38:1 0.302 0.338 0.429 0.316 0.436 0.519 0.184 0.094 0.073 0.235 0.276 0.045 0.325 0.143 0.13 PC aa C38:3 2.52 4.12 5.13 2.72 2.99 3.92 1.6 0.636 0.567 1.48 1.71 0.208 2.59 2.96 0.736 PC aa C38:4 31.1 46.4 44.7 26.7 34.9 39.7 14.2 6.27 4.1 17.5 26.6 2.96 32.1 10.8 7.48 PC aa C40:2 0.08 0.097 0.143 0.137 0.09 0.097 0.052 0.008 0.008 0.04 0.055 0.04 0.07 0.09 0.008 PC aa C40:4 0.757 1.28 1.43 0.624 0.769 0.896 0.313 0.139 0.115 0.281 0.426 0.08 0.652 0.286 0.176 PC aa C40:5 2.69 4.78 5.41 3.06 3.85 4.01 1.16 0.595 0.316 1.34 2.27 0.236 3 0.681 0.835 PC aa C40:6 17.5 27.3 26.6 15.6 22.2 18.4 6.55 4.75 2.56 7.7 14 2.03 22 5.91 5.14 PC aa C42:4 0.07 0.061 0.101 0.062 0.084 0.058 0.051 0.03 0.034 0.037 0.038 0.018 0.052 0.063 0.028 PC aa C42:5 0.085 0.114 0.117 0.067 0.097 0.103 0.063 0.038 0.024 0.07 0.08 0.03 0.07 0.049 0.036 PC ae C30:0 0.207 0.219 0.177 0.182 0.158 0.142 0.12 0.024 0.024 0.161 0.024 0.024 0.159 0.024 0.024 PC ae C30:1 0.11 0.118 0.124 0.088 0.137 0.113 0.066 0.05 0.039 0.077 0.091 0.018 0.086 0.064 0.055 PC ae C32:1 1.83 2.34 2.12 1.44 2.05 1.91 1.03 0.437 0.286 1.17 1.34 0.265 1.46 0.367 0.641 PC ae C32:2 0.255 0.284 0.221 0.224 0.337 0.289 0.188 0.095 0.019 0.184 0.189 0.019 0.224 0.113 0.105 PC ae C34:0 0.691 1.01 1.02 0.728 0.956 0.823 0.406 0.182 0.125 0.505 0.497 0.155 0.807 0.199 0.332 PC ae C34:1 4.7 6.35 6.26 4.34 5.38 5.32 2.86 1.08 0.613 3.41 3.25 0.619 4.08 1.05 1.62 PC ae C34:2 3.29 3.83 3.32 3.12 3.65 3.53 2.18 0.694 0.386 1.72 1.78 0.411 1.96 0.757 0.834 PC ae C34:3 0.99 1.2 0.967 0.938 1.53 1.24 0.618 0.297 0.168 0.497 0.767 0.106 0.665 0.295 0.262 PC ae C36:0 0.245 0.24 0.278 0.336 0.331 0.272 0.215 0.035 0.035 0.226 0.203 0.035 0.304 0.175 0.183 PC ae C36:1 1.47 2.28 2.29 1.42 1.89 2.13 0.992 0.447 0.265 0.972 1.16 0.235 1.6 0.83 0.543 PC ae C36:2 3.32 4.08 3.82 2.95 4.09 4.1 2.19 0.578 0.352 1.55 1.9 0.325 2.18 1.33 0.795 PC ae C36:3 1.47 1.67 1.37 1.66 1.73 1.71 0.977 0.316 0.173 0.714 0.884 0.178 0.976 0.422 0.334 PC ae C36:4 2.52 3.16 2.42 3.38 2.56 2.8 1.47 0.722 0.491 1.78 1.73 0.428 2.18 0.897 1.01 PC ae C36:5 2.47 3.42 2.67 2.35 3.42 4.32 1.57 0.561 0.36 1.29 1.81 0.241 1.95 0.556 0.691 PC ae C38:1 0.4 0.45 0.489 0.42 0.619 0.47 0.36 0.185 0.103 0.354 0.384 0.132 0.565 0.382 0.231 PC ae C38:2 0.365 0.535 0.723 0.397 0.548 0.479 0.281 0.1 0.097 0.218 0.201 0.057 0.317 0.503 0.123 PC ae C38:4 2.42 3.1 2.69 2.3 2.67 3.02 1.42 0.733 0.425 1.84 2.16 0.405 2.99 0.952 0.971 PC ae C38:5 2.24 3.02 2.45 3.31 2.84 3.07 1.51 0.645 0.382 1.42 1.81 0.381 2.25 0.861 0.767 PC ae C38:6 3.53 4.64 3.46 3.29 4.55 4.17 1.85 1.04 0.531 2.4 2.67 0.517 3.73 0.764 1.3 PC ae C40:4 0.444 0.518 0.543 0.433 0.492 0.486 0.34 0.334 0.272 0.384 0.449 0.338 0.473 0.42 0.279 PC ae C42:1 0.205 0.25 0.234 0.242 0.266 0.263 0.096 0.083 0.0166 0.159 0.198 0.0166 0.23 0.099 0.094 SM (OH) C14:1 0.4 0.327 0.217 0.527 0.281 0.239 0.207 0.126 0.104 0.325 0.14 0.0208 0.177 0.299 0.112 SM (OH) C16:1 0.609 0.538 0.519 0.643 0.63 0.62 0.364 0.244 0.13 0.566 0.413 0.105 0.456 0.239 0.285 SM (OH) C22:1 0.477 0.691 1.06 0.289 0.5 0.596 0.236 0.143 0.137 0.173 0.224 0.026 0.328 0.509 0.078 SM (OH) C22:2 0.237 0.276 0.328 0.174 0.235 0.263 0.123 0.079 0.082 0.156 0.064 0.0128 0.097 0.302 0.0128 SM (OH) C24:1 0.287 0.395 0.314 0.292 0.364 0.299 0.189 0.178 0.095 0.212 0.272 0.085 0.264 0.172 0.14 SM C16:0 15.6 14.6 11.1 18 11.4 12.2 8.38 5.22 3.44 10.4 6.06 2.23 8.86 7.46 4.94 SM C24:0 1.04 1.68 3.13 0.861 1.02 1.44 0.438 0.317 0.289 0.462 0.504 0.045 0.941 1.17 0.225 SM C24:1 2.75 3.84 7.24 3.19 3.11 4.74 1.64 0.694 0.619 1.71 1.49 0.219 1.92 3.71 0.515 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name PubChem KEGG Asp 5960 C00049 His 6274 C00135 Met 6137 C00073 Thr 6288 C00188 Tyr 6057 C00082 Carnosine 439224 C00386 Creatinine 588 C00791 Spermidine 1102 C00315 Spermine 1103 C00750 Taurine 1123 C00245 C0 2724480 C00318 C2 7045767 C02571 C14:1 22833575 NA C16:1 53477817 NA C16:1-OH 53481685 NA C18:1 46907933 NA C18:1-OH 53481697 NA C18:2 53477834 NA PC aa C30:2 52922434 C00157 PC aa C32:0 452110 C00157 PC aa C32:1 24778618 C00157 PC aa C32:2 24778624 C00157 PC aa C34:1 24778688 C00157 PC aa C34:2 5287971 C00157 PC aa C34:3 24778699 C00157 PC aa C36:0 24778638 C00157 PC aa C36:1 52922418 C00157 PC aa C36:2 52922420 C00157 PC aa C36:3 24778715 C00157 PC aa C38:0 24778642 C00157 PC aa C38:1 24778643 C00157 PC aa C38:3 52922473 C00157 PC aa C38:4 24778732 C00157 PC aa C40:2 24779046 C00157 PC aa C40:4 24778868 C00157 PC aa C40:5 24778871 C00157 PC aa C40:6 24778876 C00157 PC aa C42:4 53478821 C00157 PC aa C42:5 24779052 C00157 PC ae C30:0 24779275 NA PC ae C30:1 24779277 NA PC ae C32:1 53478617 C00157 PC ae C32:2 53481705 NA PC ae C34:0 11803170 NA PC ae C34:1 6443119 NA PC ae C34:2 6443157 NA PC ae C34:3 53481709 NA PC ae C36:0 24779297 NA PC ae C36:1 53481711 NA PC ae C36:2 42607428 NA PC ae C36:3 53481721 NA PC ae C36:4 53481701 NA PC ae C36:5 24779388 NA PC ae C38:1 24779301 NA PC ae C38:2 53481715 NA PC ae C38:4 6443065 NA PC ae C38:5 24779390 NA PC ae C38:6 16759366 NA PC ae C40:4 52923852 NA PC ae C42:1 53481733 NA SM (OH) C14:1 53481777 C00550 SM (OH) C16:1 53481779 C00550 SM (OH) C22:1 53481785 C00550 SM (OH) C22:2 53481787 C00550 SM (OH) C24:1 53481791 C00550 SM C16:0 5283590 C00550 SM C24:0 5283595 NA SM C24:1 44260126 C00550 METABOLITES_END #END