#METABOLOMICS WORKBENCH alg7534_20170901_124941 DATATRACK_ID:1232 STUDY_ID:ST000892 ANALYSIS_ID:AN001454 PROJECT_ID:PR000621 VERSION 1 CREATED_ON November 9, 2017, 9:57 am #PROJECT PR:PROJECT_TITLE Optimization of quantification of small molecules in intact plasma by 1D NMR PR:PROJECT_TYPE NMR pulse sequence comparison with biological samples PR:PROJECT_SUMMARY Two pulse sequences, CPMG and PROJECT, were tested to see their efficiency for PR:PROJECT_SUMMARY quantification, along as the difference between intact plasma and extracted PR:PROJECT_SUMMARY plasma. In total, 8 sets of experiments were used for quantification, 4 for the PR:PROJECT_SUMMARY intact plasma and 4 for the extracted plasma. Standard addition was used to PR:PROJECT_SUMMARY measure the concentrations in each case. PR:INSTITUTE University of Georgia PR:DEPARTMENT Complex Carbohydrates Research Center PR:LABORATORY Complex Carbohydrates Research Center PR:LAST_NAME Arthur PR:FIRST_NAME Edison PR:ADDRESS 315 Riverbend Road 30602 Athens GA PR:EMAIL aedison@uga.edu PR:PHONE +1-706-542-8156 #STUDY ST:STUDY_TITLE Comparison of T2 filters for quantification of small molecules in plasma by 1D ST:STUDY_TITLE NMR ST:STUDY_TYPE NMR development for metabolomics ST:STUDY_SUMMARY A pooled plasma sample obtained from Red Cross has been seperated into 20 ST:STUDY_SUMMARY samples. 10 of them were simply mixed with a D2O phosphate buffer, while the ST:STUDY_SUMMARY other 10 were centrifuged first, then dried and resuspended in a 90/10 H2O/D2O ST:STUDY_SUMMARY phosphate buffer. The 20 NMR samples were analysed by NMR (4 spectra per sample, ST:STUDY_SUMMARY but different pulse sequences and parameters were used for each group). Standard ST:STUDY_SUMMARY addition was used in order to measure the concentration of 5 metabolites: ST:STUDY_SUMMARY valine, lactate, glucose, phenylalanine and formate. ST:INSTITUTE Complex Carbohydrates Research Center ST:LAST_NAME Edison ST:FIRST_NAME Arthur ST:ADDRESS 315 Riverbend Road 30602 Athens GA ST:EMAIL aedison@uga.edu ST:PHONE +1-706-542-8156 ST:NUM_GROUPS 2 ST:TOTAL_SUBJECTS 20 #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 - EXPL6 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL1 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL10 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL7 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL4 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL11 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL8 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL5 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL9 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL2 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - EXPL3 Sample type:Extracted plasma SUBJECT_SAMPLE_FACTORS - PL20 Sample type:Intact plasma SUBJECT_SAMPLE_FACTORS - PL11 Sample type:Intact plasma SUBJECT_SAMPLE_FACTORS - PL17 Sample type:Intact plasma SUBJECT_SAMPLE_FACTORS - PL18 Sample type:Intact plasma SUBJECT_SAMPLE_FACTORS - PL13 Sample type:Intact plasma SUBJECT_SAMPLE_FACTORS - PL14 Sample type:Intact plasma SUBJECT_SAMPLE_FACTORS - PL16 Sample type:Intact plasma SUBJECT_SAMPLE_FACTORS - PL12 Sample type:Intact plasma SUBJECT_SAMPLE_FACTORS - PL19 Sample type:Intact plasma SUBJECT_SAMPLE_FACTORS - PL15 Sample type:Intact plasma #COLLECTION CO:COLLECTION_SUMMARY Not available #TREATMENT TR:TREATMENT_SUMMARY Not available #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Mixing 540 μL of urine with 60 μL D2O potassium buffer + DSS SP:EXTRACT_STORAGE -80 C #CHROMATOGRAPHY CH:CHROMATOGRAPHY_TYPE - CH:INSTRUMENT_NAME - CH:COLUMN_NAME - #ANALYSIS AN:ACQUISITION_PARAMETERS_FILE plasma-paper-160821/CPMG-1; plasma-paper-160822/CPMG-1 and plasma-paper-160823/CPMG-1 | plasma-paper-160821/CPMG-2; plasma-paper-160822/CPMG-2 and plasma-paper-160823/CPMG-2 | plasma-paper-160821/CPMG-3; plasma-paper-160822/CPMG-3 and plasma-paper-160823/CPMG-3 | plasma-paper-160821/PROJECT-1; plasma-paper-160822/PROJECT-1 and plasma-paper-160826/PROJECT-1 | plasma-paper-160821/NOESYPR.D plasma-paper-160822/NOESYPR1D and plasma-paper-160828/NOESYPR1D | plasma-paper-160821/PURGE; plasma-paper-160822/PURGE and plasma-paper-160828/PURGE | plasma-paper-160821/CPMG-4; plasma-paper-160822/CPMG-4 and plasma-paper-160823/CPMG-4 | plasma-paper-160821/PROJECT-2; plasma-paper-160822/PROJECT-2 and plasma-paper-160826/PROJECT-2 AN:ANALYSIS_TYPE NMR #NMR NM:INSTRUMENT_NAME FT NMR NM:INSTRUMENT_TYPE FT-NMR NM:NMR_EXPERIMENT_TYPE 1D-1H NM:NMR_COMMENTS For intact plasma | For intact plasma | For intact plasma | For intact plasma | NM:NMR_COMMENTS For extracted plasma | For extracted plasma | For extracted plasma | For NM:NMR_COMMENTS extracted plasma NM:FIELD_FREQUENCY_LOCK 2824.58 Hz | 2824.58 Hz | 2824.58 Hz | 2824.58 Hz | 2824.58 Hz | 2824.58 Hz | NM:FIELD_FREQUENCY_LOCK 2824.58 Hz | 2824.58 Hz NM:SPECTROMETER_FREQUENCY 600 MHz | 600 MHz | 600 MHz | 600 MHz | 601 MHz | 602 MHz | 603 MHz | 604 MHz NM:SPECTROMETER_FREQUENCY NMR Probe | TCI 600 H-C/N-D | TCI 600 H-C/N-D | TCI 600 H-C/N-D | TCI 600 NM:SPECTROMETER_FREQUENCY H-C/N-D | TCI 600 H-C/N-D | TCI 600 H-C/N-D | TCI 600 H-C/N-D | TCI 600 H-C/N-D NM:NMR_SOLVENT H2O+D2O (90/10) phosphate buffer | H2O+D2O (90/10) phosphate buffer | H2O+D2O NM:NMR_SOLVENT (90/10) phosphate buffer | H2O+D2O (90/10) phosphate buffer | D2O phosphate NM:NMR_SOLVENT buffer | D2O phosphate buffer | D2O phosphate buffer | D2O phosphate buffer NM:NMR_TUBE_SIZE 5 mm NM:SHIMMING_METHOD Topshim | Topshim | Topshim | Topshim | Topshim | Topshim | Topshim | Topshim NM:SHIMMING_METHOD Pulse Sequence | cpmgpr1d | cpmgpr1d | cpmgpr1d | PROJECTpr1d-1 | noesypr1d | NM:SHIMMING_METHOD zgpurge-gprefocus-2 | cpmgpr1d | PROJECTpr1d-1 NM:WATER_SUPPRESSION Presaturation NM:PULSE_WIDTH 19.94 μs | 19.94 μs | 19.94 μs | 19.94 μs | 11.82 μs | 11.82 μs | 11.82 NM:PULSE_WIDTH μs | 11.82 μs NM:POWER_LEVEL 5.5584 W | 5.5584 W | 5.5584 W | 5.5584 W | 5.5584 W | 5.5584 W | 5.5584 W | NM:POWER_LEVEL 5.5584 W NM:RECEIVER_GAIN 90.5 | 90.5 | 90.5 | 90.5 | 90.5 | 90.5 | 90.5 | 90.5 NM:OFFSET_FREQUENCY 2824.58 Hz | 2824.58 Hz | 2824.58 Hz | 2824.58 Hz | 2824.58 Hz | 2824.58 Hz | NM:OFFSET_FREQUENCY 2824.58 Hz | 2824.58 Hz NM:PRESATURATION_POWER_LEVEL 4.13E-05 | 4.13E-05 | 4.13E-05 | 4.13E-05 | 4.13E-05 | 4.13E-05 | 4.13E-05 | NM:PRESATURATION_POWER_LEVEL 4.13E-05 NM:CHEMICAL_SHIFT_REF_CPD DSS | DSS | DSS | DSS | DSS | DSS | DSS | DSS NM:TEMPERATURE 310 K | 311 K | 312 K | 313 K | 314 K | 315 K | 316 K | 317 K NM:NUMBER_OF_SCANS 32 | 32 | 32 | 32 | 32 | 32 | 32 | 32 NM:DUMMY_SCANS 4 | 4 | 4 | 4 | 4 | 4 | 4 | 4 NM:ACQUISITION_TIME 3.067 | 3.067 | 3.067 | 3.067 | 3.067 | 3.067 | 3.067 | 3.067 NM:RELAXATION_DELAY 4 s | 4 s | 4 s | 4 s | 5 s | 6 s | 7 s | 8 s NM:SPECTRAL_WIDTH 20.03 ppm | 20.03 ppm | 20.03 ppm | 20.03 ppm | 20.03 ppm | 20.03 ppm | 20.03 NM:SPECTRAL_WIDTH ppm | 20.03 ppm NM:NUM_DATA_POINTS_ACQUIRED 73728 | 73728 | 73728 | 73728 | 73728 | 73728 | 73728 | 73728 NM:REAL_DATA_POINTS 36864 | 36864 | 36864 | 36864 | 36864 | 36864 | 36864 | 36864 NM:LINE_BROADENING 0.3 Hz | 0.3 Hz | 0.3 Hz | 0.3 Hz | 0.3 Hz | 0.3 Hz | 0.3 Hz | 0.3 Hz NM:ZERO_FILLING 65536 | 65536 | 65536 | 65536 | 65536 | 65536 | 65536 | 65536 NM:APODIZATION Gaussian | Gaussian | Gaussian | Gaussian | Gaussian | Gaussian | Gaussian | NM:APODIZATION Gaussian NM:BASELINE_CORRECTION_METHOD Polynomial order 2 | Polynomial order 2 | Polynomial order 2 | Polynomial order NM:BASELINE_CORRECTION_METHOD 2 | Polynomial order 2 | Polynomial order 2 | Polynomial order 2 | Polynomial NM:BASELINE_CORRECTION_METHOD order 2 NM:CHEMICAL_SHIFT_REF_STD DSS | DSS | DSS | DSS | DSS | DSS | DSS | DSS #NMR_METABOLITE_DATA NMR_METABOLITE_DATA:UNITS μM NMR_METABOLITE_DATA_START Samples PL20 PL11 PL17 PL18 PL13 PL14 PL16 PL12 PL19 PL15 EXPL6 EXPL10 EXPL7 EXPL4 EXPL1 EXPL8 EXPL5 EXPL9 EXPL2 EXPL3 Factors Sample type:Intact plasma Sample type:Intact plasma Sample type:Intact plasma Sample type:Intact plasma Sample type:Intact plasma Sample type:Intact plasma Sample type:Intact plasma Sample type:Intact plasma Sample type:Intact plasma Sample type:Intact plasma Sample type:Extracted plasma Sample type:Extracted plasma Sample type:Extracted plasma Sample type:Extracted plasma Sample type:Extracted plasma Sample type:Extracted plasma Sample type:Extracted plasma Sample type:Extracted plasma Sample type:Extracted plasma Sample type:Extracted plasma Lactate 1 - CPMG-1 4833 6756 6055 8198 6902 5028 7437 7465 7404 6941 Lactate 2 - CPMG-1 3671 5182 4563 6216 5225 3893 5576 5642 5483 5127 Valine 1 - CPMG-1 173 229 216 277 237 177 255 254 251 232 Valine 2 - CPMG-1 132 173 162 210 179 134 196 191 189 177 Glucose 1 - CPMG-1 1454 2014 1851 2435 2111 1530 2232 2211 2219 2034 Phenylalanine 1 - CPMG-1 57 80 64 89 80 54 86 89 81 77 Phenylalanine 2 - CPMG-1 63 84 69 87 88 58 89 91 81 78 Phenylalanine 3 - CPMG-1 30 44 35 47 46 29 46 62 43 38 Formate 1 - CPMG-1 18 32 29 33 31 22 25 36 32 27 Lactate 1 - CPMG-2 3753 5039 4699 5940 4776 3904 5488 5480 5445 5102 Lactate 2 - CPMG-2 3343 4552 4345 5072 4776 3572 4889 4847 4825 4642 Valine 1 - CPMG-2 132 175 165 231 1881 135 195 196 192 175 Valine 2 - CPMG-2 107 141 133 171 147 110 158 157 153 141 Glucose 1 - CPMG-2 1045 1439 1317 1737 1505 1096 1617 1573 1559 1442 Phenylalanine 1 - CPMG-2 30 43 33 47 44 28 48 46 43 41 Phenylalanine 2 - CPMG-2 30 41 38 48 46 58 48 50 51 41 Phenylalanine 3 - CPMG-2 16 22 22 27 27 18 26 27 25 21 Formate 1 - CPMG-2 21 28 25 29 29 19 30 28 24 27 Lactate 1 - CPMG-3 3534 4944 4573 5865 4993 3608 5396 5418 5363 4853 Lactate 2 - CPMG-3 3271 4543 4312 5328 4651 3387 5023 5004 4948 4454 Valine 1 - CPMG-3 126 170 158 208 176 130 189 190 187 170 Valine 2 - CPMG-3 104 140 129 172 145 108 157 157 152 139 Glucose 1 - CPMG-3 1098 1518 1376 1795 1560 1132 1674 1631 1618 1508 Phenylalanine 1 - CPMG-3 30 41 32 47 39 25 45 47 41 38 Phenylalanine 2 - CPMG-3 32 48 30 47 42 27 42 46 39 32 Phenylalanine 3 - CPMG-3 14 19 18 22 21 16 22 20 19 26 Formate 1 - CPMG-3 19 30 22 29 24 27 27 27 30 26 Lactate 1 - PROJECT-1 3745 5091 4645 6119 5200 3895 5594 5568 5463 5096 Lactate 2 - PROJECT-1 3354 4480 4138 5399 4632 3571 4961 4939 4861 4514 Valine 1 - PROJECT-1 130 173 160 212 180 134 193 192 188 170 Valine 2 - PROJECT-1 105 140 129 173 146 108 156 156 152 140 Glucose 1 - PROJECT-1 1176 1626 1485 1960 1676 1238 1810 1770 1785 1622 Phenylalanine 1 - PROJECT-1 27 38 29 42 37 25 43 43 38 37 Phenylalanine 2 - PROJECT-1 25 31 25 37 34 29 37 36 35 36 Phenylalanine 3 - PROJECT-1 13 15 12 18 20 13 20 18 18 16 Formate 1 - PROJECT-1 19 24 24 26 26 21 30 31 32 22 Lactate 1 - NOESYPR1D 5528 5232 5403 5445 5476 5483 5354 5764 5965 5538 Lactate 2 - NOESYPR1D 4197 4752 4933 5201 5258 5137 5324 5531 5490 5291 Valine 1 - NOESYPR1D 301 311 291 302 299 305 305 324 333 315 Valine 2 - NOESYPR1D 222 237 216 225 219 223 227 242 248 233 Glucose 1 - NOESYPR1D 1768 1619 1561 1679 1687 1656 1676 1769 1872 1769 Phenylalanine 1 - NOESYPR1D 59 64 64 63 56 58 68 68 73 65 Phenylalanine 2 - NOESYPR1D 68 72 68 70 64 64 83 76 79 77 Phenylalanine 3 - NOESYPR1D 45 49 47 48 46 46 55 54 58 52 Formate 1 - NOESYPR1D 20 35 25 40 29 25 31 34 26 29 Lactate 1 - PURGE 5495 5185 5367 5393 5422 5408 5323 5725 5924 5483 Lactate 2 - PURGE 4800 4630 4690 4930 5059 5015 5059 5564 5374 5267 Valine 1 - PURGE 290 297 283 292 287 288 294 308 319 300 Valine 2 - PURGE 211 223 209 214 207 207 217 224 234 218 Glucose 1 - PURGE 1708 1572 1501 1627 1674 1649 1623 1723 1831 1696 Phenylalanine 1 - PURGE 60 62 63 63 58 60 66 66 72 65 Phenylalanine 2 - PURGE 61 67 63 69 67 62 70 72 78 70 Phenylalanine 3 - PURGE 44 43 41 47 44 47 49 50 54 51 Formate 1 - PURGE 25 27 24 26 35 30 33 31 31 35 Lactate 1 - CPMG-4 5160 4865 4991 5104 5037 5098 5018 5363 5560 5193 Lactate 2 - CPMG-4 4463 4316 4347 4589 4805 4733 4755 5186 5186 4831 Valine 1 - CPMG-4 200 190 198 200 201 204 200 212 212 209 Valine 2 - CPMG-4 145 138 143 146 144 147 147 154 154 152 Glucose 1 - CPMG-4 1368 1228 1323 1371 1245 1290 1273 1302 1302 1390 Phenylalanine 1 - CPMG-4 51 47 51 53 48 52 52 52 61 58 Phenylalanine 2 - CPMG-4 50 40 47 49 43 43 50 50 56 55 Phenylalanine 3 - CPMG-4 36 33 37 38 33 35 40 38 46 41 Formate 1 - CPMG-4 26 23 25 30 26 30 31 34 32 28 Lactate 1 - PROJECT-2 5124 4822 4947 5059 5038 5037 4969 5309 5502 5114 Lactate 2 - PROJECT-2 4268 4460 4568 4460 4640 4536 4803 5027 4890 4936 Valine 1 - PROJECT-2 202 183 191 199 198 202 196 207 219 204 Valine 2 - PROJECT-2 143 133 138 144 140 145 142 149 164 147 Glucose 1 - PROJECT-2 1362 1234 1259 1349 1331 1338 1335 1372 1500 1398 Phenylalanine 1 - PROJECT-2 50 46 52 51 50 52 55 53 60 55 Phenylalanine 2 - PROJECT-2 44 44 51 45 46 48 55 50 55 55 Phenylalanine 3 - PROJECT-2 33 37 39 37 33 37 43 38 46 45 NMR_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name Lactate 1 - CPMG-1 Lactate 2 - CPMG-1 Valine 1 - CPMG-1 Valine 2 - CPMG-1 Glucose 1 - CPMG-1 Phenylalanine 1 - CPMG-1 Phenylalanine 2 - CPMG-1 Phenylalanine 3 - CPMG-1 Formate 1 - CPMG-1 Lactate 1 - CPMG-2 Lactate 2 - CPMG-2 Valine 1 - CPMG-2 Valine 2 - CPMG-2 Glucose 1 - CPMG-2 Phenylalanine 1 - CPMG-2 Phenylalanine 2 - CPMG-2 Phenylalanine 3 - CPMG-2 Formate 1 - CPMG-2 Lactate 1 - CPMG-3 Lactate 2 - CPMG-3 Valine 1 - CPMG-3 Valine 2 - CPMG-3 Glucose 1 - CPMG-3 Phenylalanine 1 - CPMG-3 Phenylalanine 2 - CPMG-3 Phenylalanine 3 - CPMG-3 Formate 1 - CPMG-3 Lactate 1 - PROJECT-1 Lactate 2 - PROJECT-1 Valine 1 - PROJECT-1 Valine 2 - PROJECT-1 Glucose 1 - PROJECT-1 Phenylalanine 1 - PROJECT-1 Phenylalanine 2 - PROJECT-1 Phenylalanine 3 - PROJECT-1 Formate 1 - PROJECT-1 Lactate 1 - NOESYPR1D Lactate 2 - NOESYPR1D Valine 1 - NOESYPR1D Valine 2 - NOESYPR1D Glucose 1 - NOESYPR1D Phenylalanine 1 - NOESYPR1D Phenylalanine 2 - NOESYPR1D Phenylalanine 3 - NOESYPR1D Formate 1 - NOESYPR1D Lactate 1 - PURGE Lactate 2 - PURGE Valine 1 - PURGE Valine 2 - PURGE Glucose 1 - PURGE Phenylalanine 1 - PURGE Phenylalanine 2 - PURGE Phenylalanine 3 - PURGE Formate 1 - PURGE Lactate 1 - CPMG-4 Lactate 2 - CPMG-4 Valine 1 - CPMG-4 Valine 2 - CPMG-4 Glucose 1 - CPMG-4 Phenylalanine 1 - CPMG-4 Phenylalanine 2 - CPMG-4 Phenylalanine 3 - CPMG-4 Formate 1 - CPMG-4 Lactate 1 - PROJECT-2 Lactate 2 - PROJECT-2 Valine 1 - PROJECT-2 Valine 2 - PROJECT-2 Glucose 1 - PROJECT-2 Phenylalanine 1 - PROJECT-2 Phenylalanine 2 - PROJECT-2 Phenylalanine 3 - PROJECT-2 METABOLITES_END #END