#METABOLOMICS WORKBENCH chalermrojCS_20231106_074005 DATATRACK_ID:4441 STUDY_ID:ST002970 ANALYSIS_ID:AN004879 PROJECT_ID:PR001849 VERSION 1 CREATED_ON November 6, 2023, 8:59 am #PROJECT PR:PROJECT_TITLE Fatty alcohol production PR:PROJECT_SUMMARY Part 1/3 of XR/lactose system demonstrated in E. coli PR:INSTITUTE Vidyasirimedhi Institute of Science and Technology PR:LAST_NAME Sutthaphirom PR:FIRST_NAME Chalermroj PR:ADDRESS 555, Moo 1, Payubnai, Wangchan, Rayong, 21210, Thailand PR:EMAIL chalermroj.s_s19@vistec.ac.th PR:PHONE (+66)063-9639915 #STUDY ST:STUDY_TITLE fatty alcohol T90min ST:STUDY_SUMMARY Untargeted metabolomics of fatty alcohol producing strains at time 90 min of ST:STUDY_SUMMARY bioconversion ST:INSTITUTE Vidyasirimedhi Institute of Science and Technology ST:LAST_NAME Sutthaphirom ST:FIRST_NAME Chalermroj ST:ADDRESS 555, Moo 1, Payubnai, Wangchan, Rayong, 21210, Thailand ST:EMAIL chalermroj.s_s19@vistec.ac.th ST:PHONE (+66)063-9639915 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 8 #SUBJECT SU:SUBJECT_TYPE Bacteria SU:SUBJECT_SPECIES Escherichia coli SU:TAXONOMY_ID 562 SU:GENOTYPE_STRAIN BL21 (DE3) SU:CELL_BIOSOURCE_OR_SUPPLIER Novagen #FACTORS #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 - FAR_T90_min-1 Strain:FAR SUBJECT_SAMPLE_FACTORS - FAR_T90_min-2 Strain:FAR SUBJECT_SAMPLE_FACTORS - FAR_T90_min-3 Strain:FAR SUBJECT_SAMPLE_FACTORS - FAR_T90_min-4 Strain:FAR SUBJECT_SAMPLE_FACTORS - XR_T90_min-1 Strain:XR SUBJECT_SAMPLE_FACTORS - XR_T90_min-2 Strain:XR SUBJECT_SAMPLE_FACTORS - XR_T90_min-3 Strain:XR SUBJECT_SAMPLE_FACTORS - XR_T90_min-4 Strain:XR #COLLECTION CO:COLLECTION_SUMMARY Samples were quenched by cold methanol and were extracted metabolites by cold CO:COLLECTION_SUMMARY methanol method. CO:SAMPLE_TYPE Bacterial cells #TREATMENT TR:TREATMENT_SUMMARY Cells were incubated with 10 mM lactose in Kpi buffer at 25˚C for 90 min #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Intracellular metabolites were extracted by cold methanol method. The SP:SAMPLEPREP_SUMMARY supernatants were lyophilized and reconstituted in 50% acetonitrile/water. #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE HILIC CH:INSTRUMENT_NAME Agilent 6560 CH:COLUMN_NAME Agilent Poroshell 120 HILIC-Z (150 x 2.1 mm, 2.7 µm) CH:SOLVENT_A 10 mM ammonium acetate pH 9.0 CH:SOLVENT_B 10 mM ammonium acetate in 85% acetonitrile/water pH 9.0 CH:FLOW_GRADIENT 0 min: 96%B, 24 min: 65%B CH:FLOW_RATE 0.3 mL/min CH:COLUMN_TEMPERATURE 35˚C #ANALYSIS AN:ANALYSIS_TYPE MS #MS MS:INSTRUMENT_NAME Agilent 6560 Ion Mobility MS:INSTRUMENT_TYPE QTOF MS:MS_TYPE ESI MS:ION_MODE NEGATIVE MS:MS_COMMENTS Raw MS data files (.d) were first demultiplexed using the Agilent MS:MS_COMMENTS De-multiplexing tool (Version 1.0, Agilent Technologies). The demultiplexing MS:MS_COMMENTS data files (.DeMP.d) were recalibrated using IM–MS Reprocessor (Version MS:MS_COMMENTS B.08.00, Agilent Technologies). The reference masses used for mass calibration MS:MS_COMMENTS were m/z 112.985587 and 1033.988109. The CCS calibration was performed by the MS:MS_COMMENTS IM–MS Browser software (Version 10.0, Agilent Technologies). #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS abundance MS_METABOLITE_DATA_START Samples FAR_T90_min-1 FAR_T90_min-2 FAR_T90_min-3 FAR_T90_min-4 XR_T90_min-1 XR_T90_min-2 XR_T90_min-3 XR_T90_min-4 Factors Strain:FAR Strain:FAR Strain:FAR Strain:FAR Strain:XR Strain:XR Strain:XR Strain:XR D-Gluconic acid 50753408 49065720 48756120 49851332 73515384 69048048 67610552 67505840 3-oxo-hexanoyl-CoA 58485512 51493848 45640508 42374400 31996658 25567920 22671876 20896008 GSH / Glutathione 15465056 13133888 11507527 9207109 23967672 19013876 15463257 13002889 UDP-L-Ara4FN 11385638 10439795 9899910 9102701 19388116 16943988 16119108 15220594 N-stearoyl taurine 4536250 4592267 4824536 4634150 15772745 14904514 15387671 14795096 UDPG / Uridine 5'-diphosphoglucose 6394396 5843365 5692712 5155392 15295039 13426593 12669815 12185931 ADP / Adenosine 5'-diphosphate 6848601 6325008 6079824 6277373 10879929 9074512 8485527 7755792 D-Glucose 6-phosphate 9316200 8065931 7684630 7530315 5361903 4762682 4371415 4326650 Adenylosuccinic acid 6074259 4530166 4005703 2799391 8457253 6405143 5540189 4852531 L-Tyrosine 4944478 4706057 4649312 4688136 3003869 2856764 2782012 2778962 2-Keto-3-deoxy-D-gluconic acid 3157896 2937049 2170335 1993815 4436841 4681198 4485047 2912518 S-Acetylphosphopantetheine 1224252 1184693 1018278 497437 4460061 3815495 3849129 3456505 Lactitol 1 1 40725 1 3401429 3287732 3119931 3049856 4-Phospho-D-erythronate 1 245103 398437 691419 2853980 2337664 2469629 2824609 N-Glycolylneuraminic acid 1134581 906950 810308 828915 2344700 1823344 1557915 1432545 NAD 1651536 1641600 1675607 1508159 1212336 1150226 1192866 1277399 OPC4-CoA 1241990 1085300 1017616 803991 1954619 1729258 1621982 1488719 D-Sorbitol 1 1 1 1 1634316 1675453 1674035 1659553 Pantoic acid 829953 800741 795850 803497 1299527 1165060 1101323 1117130 DHAP(18:0e) 400601 424484 421555 419936 1294799 1189597 1017330 1150656 α-D-Glucose 1 894554 836392 1 1868234 1504132 935078 1 D-Sedoheptulose-7-phosphate 1215197 1 1088493 1171589 355572 322852 1 1 Glutathionylspermine 262189 177602 182552 382845 755341 805100 936858 1008452 L-Glutamic acid 713395 663967 694216 710217 945261 860018 843335 861467 dTTP / 2'-Deoxythymidine 5'-triphosphate 638671 588874 519462 601146 1475830 1107446 1 949729 Adenosine 5'-triphosphate (ATP) 258169 217494 231303 281535 788840 593837 563846 597187 β-D-Fructose 1,6-bisphosphate 407050 368710 331960 1 1 778903 776434 816316 N-Acetyl-L-glutamic acid 462328 384767 337820 322344 840478 610708 562100 497291 SAH / S-Adenosyl-L-homocysteine 514985 524562 492096 552293 258435 250696 245718 250974 D-Ribulose 5-phosphate 698966 661889 1 606435 1 360769 325350 1 NADPH 326335 278596 237913 176754 777539 533712 422414 348668 Acetyl-CoA 1 230969 222460 1 500174 414565 383668 377916 UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine 156593 190683 168168 1 400989 389558 369623 370221 UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-L-lysine 344479 299211 274864 267475 159511 118280 114457 97258 L-Fuculose 230575 244565 232421 240289 1 389347 387926 389187 D-Fructose 6-phosphate 290758 1 219137 225601 411175 411856 1 361486 Sedoheptulose 1,7-bisphosphate 129921 109362 128178 1 359491 271265 311252 223881 L-Valine 1 222238 1 215229 291980 272807 289796 289023 D-myo-Inositol-1,3,4-triphosphate 233533 176711 130427 480627 1 83541 1 1 5'-Adenylyl sulfate (APS) 204479 229591 268391 314395 45959 51490 1 70894 L-Histidine 1 1 106976 1 1 396687 265378 345856 D-Glycerate 3-phosphate 1 1 1 1 410003 332025 342679 1 L-Fucose 1-phosphate 167828 158580 1 118010 256816 257697 269581 258448 Guanosine 3',5'-bis(diphosphate) 1 1 1 163467 311855 256260 255555 150007 Sorbitol-6-phosphate 1 1 1 1 1 335372 299045 264984 DL-3-amino-isobutanoic acid 1 1 1 1 1 244983 262264 257517 N-Succinyl-L-glutamate 288909 245574 1 208751 255234 198841 1 1 ADP-ribose 1″-2″ cyclic phosphate 1 1 1 1 447675 165988 46512 137442 1,4-beta-D-Glucan 92968 100402 90373 71069 200223 174029 154454 144946 beta-Lactose 156866 156290 164858 129909 104608 93767 94878 97602 3-Methylcrotonyl-CoA 170078 148592 139362 129889 92119 67337 1 1 Myrsinone 80603 84479 294402 103906 1 256751 1 1 6-Phosphogluconic acid 1 1 77946 1 233520 149111 231345 1 Gulonic acid 1 1 1 1 238517 154787 183553 32156 Trehalose 6-phosphate 104472 93144 1 1 209170 141439 120395 107618 3-hydroxy-hexadecanoic acid 156685 1 152322 175131 36521 16688 1 1 2-Isopropylmalic acid 87338 85478 87128 94027 177022 146575 136477 1 NADH 99971 74165 45248 1 195864 117456 75837 43006 Succinoadenosine 1 37894 1 1 196010 107669 84665 26293 GDP-L-fucose 47687 1 1 1 76072 116244 1 129854 Glutamyl-gamma-glutamate 1 1 30838 1 166862 77034 46020 23287 KAPA 1 1 1 1 70140 66951 67088 73327 UDP-2,4-bis(acetamido)-2,4,6-trideoxy-beta-L-altropyranose 1 1 1 1 66537 73821 63033 59921 D-Pantetheine 4'-phosphate 51244 1 1 1 92126 92764 1 79622 dTDP-L-rhamnose 1 1 1 1 89989 76962 72440 1 Acetyl adenylate 1 3034 1 1 40133 31449 32744 20162 Coenzyme A (CoA) 28082 25656 22613 1 51011 55358 1 1 Oleoyl-CoA 1 1 1 1 15721 26657 18006 10401 GSSG / L-Gluthathione (oxidized) 7478 1 1 1 1 12125 6119 34509 2-Dehydro-3-deoxy-6-phospho-D-gluconate 2249726 1961212 1803977 1599133 1529548 1 1 1096723 10-formyldihydrofolate 1186779 1215621 1240861 1189742 1 1 1 1 Dihydroxyacetone (glycerone) 628291 595633 619738 569728 1 1 276923 1 dCMP / 2'-Deoxycytidine 5'-monophosphate 483602 476804 456225 395757 368118 1 392330 1 UDP / Uridine 5'-diphosphate 292948 297672 298891 310359 1 1 1 1 4-Phosphopantothenoylcysteine 251446 225497 250541 230985 80167 1 80358 71429 O-Phospho-4-hydroxy-L-threonine 294093 236672 224987 186884 66917 1 1 1 L-Phenylalanine 179760 165042 113144 1 43862 1 110795 57539 5'-Methylthioadenosine 125428 121686 1 103801 1 1 1 1 4-Hydroxyphenylacetyl-CoA 108680 92077 78911 61703 21701 1 12775 1 2-Deoxy-2,3-dehydro-N-acetylneuraminic acid 93972 73658 68139 1 1 1 1 1 Phosphoribulosylformimino-AICAR-P 51981 46400 47504 40337 1 1 1 22652 Oleic acid (C18:1) 7134 1 36788 114592 97488 1 1 1 Hexanoyl-CoA 49925 33703 20048 14972 1 1 1 1 2-Octaprenylphenol 23015 26398 34122 7261 15111 1 1 1 3-Oxohexanoyl-coenzyme A 20894 9988 1 14628 1 1 1 1 ADP-glucose 5147 12881 1 16393 1 1 1 1 D-Pantothenic acid 1 1 710448 1 1684375 1 1102384 913820 Citric acid 1 78333 34073 113267 1 1 1 1 D-Tagatose 1,6-bisphosphate 1 1 1 1 2818617 1 2162629 1991458 Palmitic acid (C16:0) 1 1 1 27599 33192 1 89375 85645 2-oxo-octadecanoic acid 1 1 1 1 147429 1 18583 18405 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Mass Retention Time DT CCS Ion Species D-Gluconic acid 196.0594 5.5970817 15.543831 133.40784 [M-H]- 3-oxo-hexanoyl-CoA 879.1738 13.998033 32.619984 265.756 [M-H]- GSH / Glutathione 307.0794 8.640127 19.413515 162.73793 [M-H]- UDP-L-Ara4FN 563.0437 8.529126 26.16457 215.04251 [M-H]- N-stearoyl taurine 391.2808 2.1340172 23.733116 197.10179 [M-H]- UDPG / Uridine 5'-diphosphoglucose 566.0386 8.552127 25.257416 207.56662 [M-H]- ADP / Adenosine 5'-diphosphate 427.0193 11.567116 22.2154 183.9895 [M-H]- D-Glucose 6-phosphate 260.0258 12.528092 18.777527 157.14403 [M+CH3COO]- Adenylosuccinic acid 463.062 16.117887 22.508837 185.96841 [M-H]- L-Tyrosine 181.0754 4.057051 16.78737 144.817 [M-H]- 2-Keto-3-deoxy-D-gluconic acid 178.0481 3.4940398 17.500862 148.50157 [M+CH3COO]- S-Acetylphosphopantetheine 400.0972 5.6640835 21.865828 181.47348 [M-H]- Lactitol 344.1282 6.690005 21.073416 175.83615 [M-H]- 4-Phospho-D-erythronate 216.0033 13.417727 23.996334 202.06258 [M+CH3COO]- N-Glycolylneuraminic acid 325.0964 11.0461235 19.71215 164.85313 [M-H]- NAD 663.0908 9.871132 27.305996 223.60988 [M-H]- OPC4-CoA 987.2933 18.170662 19.19987 312.4584 [M-2H]-2 D-Sorbitol 182.0807 3.891033 15.2446 131.47571 [M-H]- Pantoic acid 148.0749 2.6070242 14.598794 127.84874 [M-H]- DHAP(18:0e) 422.2732 2.1560173 24.551924 203.39308 [M-H]- α-D-Glucose 180.0633 5.1039886 15.360388 132.57278 [M-H]- D-Sedoheptulose-7-phosphate 290.0348 12.512915 26.55959 217.6611 [2M+CH3COO]- Glutathionylspermine 491.2927 2.7440267 26.574968 219.17014 [M-H]- L-Glutamic acid 147.0533 8.704128 14.221146 124.61585 [M-H]- dTTP / 2'-Deoxythymidine 5'-triphosphate 481.976 11.586085 22.443483 185.22055 [M-H]- Adenosine 5'-triphosphate (ATP) 506.981 12.705087 22.866 188.4474 [M-H]- β-D-Fructose 1,6-bisphosphate 339.9902 16.63812 18.611189 155.38335 [M-H]- N-Acetyl-L-glutamic acid 189.0631 9.32213 15.967872 137.36195 [M-H]- SAH / S-Adenosyl-L-homocysteine 384.1257 4.069051 21.270578 176.77916 [M-H]- D-Ribulose 5-phosphate 230.0181 12.526491 18.718563 159.11653 [M-H]- NADPH 745.0693 13.896038 27.469603 224.44519 [M-H]- Acetyl-CoA 809.1029 11.02888 30.516432 248.9622 [M-H]- UDP-3-O-(3-hydroxytetradecanoyl)-N-acetylglucosamine 833.2598 3.2940176 34.049007 277.62717 [M-H]- UDP-N-acetylmuramoyl-L-alanyl-γ-D-glutamyl-L-lysine 1007.2708 15.063971 34.563374 281.0242 [M-H]- L-Fuculose 164.0698 3.579042 14.77704 128.3882 [M-H]- D-Fructose 6-phosphate 260.0274 11.407102 17.614397 148.79292 [M-H]- Sedoheptulose 1,7-bisphosphate 369.9986 16.988752 19.461134 161.96654 [M-H]- L-Valine 117.0799 4.282067 13.986423 125.08248 [M-H]- D-myo-Inositol-1,3,4-triphosphate 419.9687 12.53107 21.016758 174.16202 [M-H]- 5'-Adenylyl sulfate (APS) 427.0254 13.169016 23.525927 194.08961 [M+CH3COO]- L-Histidine 155.0698 7.5169964 14.790546 129.05432 [M-H]- D-Glycerate 3-phosphate 185.9889 12.416893 20.145311 167.62294 [2M-H]- L-Fucose 1-phosphate 244.0299 8.550223 23.876722 196.96988 [2M-H]- Guanosine 3',5'-bis(diphosphate) 602.9412 9.848241 27.657995 226.49117 [M+CH3COO]- Sorbitol-6-phosphate 262.0426 11.776326 17.164928 144.94606 [M-H]- DL-3-amino-isobutanoic acid 103.0645 8.709167 13.347957 120.96411 [M-H]- N-Succinyl-L-glutamate 247.0685 12.647264 18.934294 158.72498 [M+CH3COO]- ADP-ribose 1″-2″ cyclic phosphate 621.0417 11.000107 27.546463 225.88779 [M-H]- 1,4-beta-D-Glucan 536.1599 16.982803 26.719133 219.85837 [M-H]- beta-Lactose 342.1111 6.629101 20.497551 171.07408 [M-H]- 3-Methylcrotonyl-CoA 849.1816 14.3257675 31.278498 254.9731 [M-H]- Myrsinone 294.1817 3.6160438 21.425121 179.91333 [M-H]- 6-Phosphogluconic acid 276.0209 14.335187 17.16641 144.60117 [M-H]- Gulonic acid 196.0573 8.548097 15.54976 133.45872 [M-H]- Trehalose 6-phosphate 422.0716 12.987287 21.662104 179.4764 [M-H]- 3-hydroxy-hexadecanoic acid 272.2343 2.1680236 20.581793 173.44727 [M-H]- 2-Isopropylmalic acid 176.0695 4.23805 15.159723 131.04503 [M-H]- NADH 665.104 8.095047 26.928555 220.50781 [M-H]- Succinoadenosine 383.0991 16.126036 15.201367 126.39945 [M-H]- GDP-L-fucose 589.0643 8.969198 26.49925 217.56216 [M-H]- Glutamyl-gamma-glutamate 275.1082 9.58093 18.619072 156.84682 [M-H]- KAPA 187.122 3.0900223 16.643473 143.26292 [M-H]- UDP-2,4-bis(acetamido)-2,4,6-trideoxy-beta-L-altropyranose 632.124 5.670059 25.973011 212.91412 [M-H]- D-Pantetheine 4'-phosphate 358.0946 15.699334 21.102253 175.81647 [M-H]- dTDP-L-rhamnose 548.0644 8.540016 26.024124 214.02806 [M-H]- Acetyl adenylate 389.0737 9.495082 31.256535 255.1661 [2M-H]- Coenzyme A (CoA) 767.0951 12.302777 29.86192 243.84985 [M-H]- Oleoyl-CoA 1031.3384 6.684074 20.209263 328.6728 [M-2H]-2 GSSG / L-Gluthathione (oxidized) 612.132 16.316067 26.543365 217.73698 [M-H]- 2-Dehydro-3-deoxy-6-phospho-D-gluconate 258.0104 9.517144 22.475931 185.15044 [2M-H]- 10-formyldihydrofolate 471.1464 12.785075 25.551422 210.30661 [M+CH3COO]- Dihydroxyacetone (glycerone) 90.0332 4.0500574 20.904135 192.2939 [M-H]- dCMP / 2'-Deoxycytidine 5'-monophosphate 307.0531 10.944074 19.458555 163.1157 [M-H]- UDP / Uridine 5'-diphosphate 403.9957 13.988997 20.852995 173.02072 [M-H]- 4-Phosphopantothenoylcysteine 402.0773 4.0090566 21.55414 178.8602 [M-H]- O-Phospho-4-hydroxy-L-threonine 215.0222 12.715906 18.53608 156.15019 [M+CH3COO]- L-Phenylalanine 165.0802 3.6590235 16.171059 140.4193 [M-H]- 5'-Methylthioadenosine 297.0875 8.8654175 18.91549 158.79185 [M-H]- 4-Hydroxyphenylacetyl-CoA 901.1521 13.995893 19.001802 309.6478 [M-2H]-2 2-Deoxy-2,3-dehydro-N-acetylneuraminic acid 291.0953 12.914823 18.617498 156.43251 [M-H]- Phosphoribulosylformimino-AICAR-P 577.0961 15.229123 25.722004 211.2856 [M-H]- Oleic acid (C18:1) 282.2551 2.2660315 20.95463 176.29137 [M-H]- Hexanoyl-CoA 865.1926 11.08614 32.518864 264.99896 [M-H]- 2-Octaprenylphenol 638.53 3.5098457 32.155697 263.49957 [M-H]- 3-Oxohexanoyl-coenzyme A 879.1646 16.140905 32.59869 265.58264 [M-H]- ADP-glucose 589.0934 7.07629 27.5063 225.82336 [M-H]- D-Pantothenic acid 219.1109 3.8400187 22.746052 193.83968 [M-H]- Citric acid 192.0278 13.15463 14.884776 127.9282 [M-H]- D-Tagatose 1,6-bisphosphate 339.9899 17.11093 18.589087 155.19904 [M-H]- Palmitic acid (C16:0) 256.2401 2.515042 20.095573 169.84985 [2M-H]- 2-oxo-octadecanoic acid 298.2487 2.1650162 21.34894 179.16724 [M-H]- METABOLITES_END #END