#METABOLOMICS WORKBENCH amitch_20151007_9165841_mwtab.txt DATATRACK_ID:387 STUDY_ID:ST000251 ANALYSIS_ID:AN000397 PROJECT_ID:PR000203 VERSION 1 CREATED_ON 2016-09-17 #PROJECT PR:PROJECT_TITLE Intracellular Amino Acid levels in response to MYC PR:PROJECT_TYPE Targeted LC-MS Metabolomics PR:PROJECT_SUMMARY Hypothesis:MYC is suppressing the autophagy pathway which leads to impaired PR:PROJECT_SUMMARY of proteins and reduced free Amino Acids in the cells. PR:INSTITUTE Moffitt Cancer Center PR:DEPARTMENT Tumor Biology PR:LAST_NAME Cleveland PR:FIRST_NAME John PR:ADDRESS 12902 Magnolia Dr PR:EMAIL John.Cleveland@moffitt.org PR:PHONE 813 745 3888 PR:FUNDING_SOURCE NIH #STUDY ST:STUDY_TITLE Amino Acid levels in preB cells under starvation ST:STUDY_TYPE treatment ST:STUDY_SUMMARY pre B cells from wt and EuMyc mice were grown in normal media and then placed ST:STUDY_SUMMARY 2hrs in EBSS. ST:INSTITUTE University of Florida ST:DEPARTMENT SECIM ST:LAST_NAME Schaub ST:FIRST_NAME Franz ST:ADDRESS R3-226 Academic Research Building, Department of Biochemistry and Molecular ST:ADDRESS PO Box 100245, Gainesville, FL 32610-0245 ST:EMAIL Franz.Schaub@moffitt.org ST:PHONE - ST:NUM_GROUPS 4 ST:TOTAL_SUBJECTS 12 #SUBJECT SU:SUBJECT_TYPE Animal cells SU:SUBJECT_SPECIES Mus musculus SU:TAXONOMY_ID 10090 SU:ANIMAL_ANIMAL_SUPPLIER inhouse breeding SU:CELL_BIOSOURCE_OR_SUPPLIER BM derived B cells SU:CELL_STRAIN_DETAILS wt and EuMyc SU:CELL_PRIMARY_IMMORTALIZED primary SU:SPECIES_GROUP Mammal #SUBJECT_SAMPLE_FACTORS: SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data SUBJECT_SAMPLE_FACTORS - CC268_EBSS1 Treatment:EuMyc transgene | media:EBSS SUBJECT_SAMPLE_FACTORS - CC268_EBSS2 Treatment:EuMyc transgene | media:EBSS SUBJECT_SAMPLE_FACTORS - CC268_EBSS3 Treatment:EuMyc transgene | media:EBSS SUBJECT_SAMPLE_FACTORS - CC268_N1 Treatment:EuMyc transgene | media:normal media SUBJECT_SAMPLE_FACTORS - CC268_N2 Treatment:EuMyc transgene | media:normal media SUBJECT_SAMPLE_FACTORS - CC268_N3 Treatment:EuMyc transgene | media:normal media SUBJECT_SAMPLE_FACTORS - CC267_EBSS1 Treatment:wt | media:EBSS SUBJECT_SAMPLE_FACTORS - CC267_EBSS2 Treatment:wt | media:EBSS SUBJECT_SAMPLE_FACTORS - CC267_EBSS3 Treatment:wt | media:EBSS SUBJECT_SAMPLE_FACTORS - CC267_N1 Treatment:wt | media:normal media SUBJECT_SAMPLE_FACTORS - CC267_N2 Treatment:wt | media:normal media SUBJECT_SAMPLE_FACTORS - CC267_N3 Treatment:wt | media:normal media #COLLECTION CO:COLLECTION_SUMMARY Cells were counted, washed with cold PBS and then flash-frozen in liquid N2 CO:SAMPLE_TYPE cells CO:VOLUMEORAMOUNT_COLLECTED 0.5.00E+07 cells CO:STORAGE_VIALS screw caps #TREATMENT TR:TREATMENT_SUMMARY Cells were incubated for 2hrs in EBSS at 37C. TR:CELL_MEDIA 45%DMEM, 45%IMDM, 10%FCS, Q, PS, Sodium Pyruvate, beta mercaptoethanol and EBSS TR:CELL_MEDIA 10% dialized FBS TR:CELL_HARVESTING washed, and pellet flashfroozen in liquid N2 TR:CELL_PCT_CONFLUENCE 2xE06 per ml #SAMPLEPREP SP:SAMPLEPREP_SUMMARY Amino acid SP:SAMPLEPREP_PROTOCOL_FILENAME SB_AA_Assay.pdf #CHROMATOGRAPHY CH:CHROMATOGRAPHY_SUMMARY Amino Acid CH:CHROMATOGRAPHY_TYPE Reversed phase MS:INSTRUMENT_NAME Agilent 6490 QQQ CH:COLUMN_NAME Waters AccQ Tag (100 x 2mm, 1.7um) CH:METHODS_FILENAME SB_AA_Assay.pdf #ANALYSIS AN:ANALYSIS_TYPE MS AN:LABORATORY_NAME Sanford Burnham AN:DETECTOR_TYPE Triple Quadrupole #MS MS:INSTRUMENT_NAME Agilent 6490 QQQ MS:INSTRUMENT_TYPE Triple quadrupole MS:MS_TYPE ESI MS:ION_MODE POSITIVE MS:MS_COMMENTS Amino Acids #MS_METABOLITE_DATA MS_METABOLITE_DATA:UNITS pmol/million cells MS_METABOLITE_DATA_START Samples CC268_EBSS1 CC268_EBSS2 CC268_EBSS3 CC268_N1 CC268_N2 CC268_N3 CC267_EBSS1 CC267_EBSS2 CC267_EBSS3 CC267_N1 CC267_N2 CC267_N3 Factors Treatment:EuMyc transgene | media:EBSS Treatment:EuMyc transgene | media:EBSS Treatment:EuMyc transgene | media:EBSS Treatment:EuMyc transgene | media:normal media Treatment:EuMyc transgene | media:normal media Treatment:EuMyc transgene | media:normal media Treatment:wt | media:EBSS Treatment:wt | media:EBSS Treatment:wt | media:EBSS Treatment:wt | media:normal media Treatment:wt | media:normal media Treatment:wt | media:normal media Alanine 286.1697 325.3258 274.6649 150.3779 167.2620 Arginine 6.4687 7.0423 7.3493 53.6907 53.4811 47.9826 6.9324 5.5625 6.1154 39.5995 37.8744 Asparagine 55.3738 59.4364 56.9143 38.5385 46.7229 41.0002 Aspartic Acid 144.5106 149.8918 134.1733 548.4718 505.6645 520.8316 141.6219 128.0513 128.5390 358.8802 449.5085 431.9556 Citrulline Glutamic Acid 505.8097 452.5393 522.7460 1618.2563 1831.7335 1844.1606 365.9140 348.5579 377.9552 1113.5555 1185.7408 1178.8394 Glutamine 2696.7081 2837.0207 2669.1879 2145.4604 2579.7559 2459.9461 Glycine 289.8055 330.7167 324.9333 880.4140 1006.6005 897.9364 173.7769 181.0660 152.0332 458.6096 522.0940 489.4995 Histidine 30.6960 33.7524 29.6564 24.8340 28.7767 22.4751 Isoleucine 95.8893 129.8472 95.3572 72.2414 87.9081 77.9505 Leucine 94.8523 109.4593 109.8084 65.0017 81.7588 72.7164 Lysine Methionine 96.2030 101.7481 95.5282 88.1543 92.3585 89.1620 Ornithine Phenylalanine 55.9604 75.1085 51.9415 37.3831 39.7466 40.4254 Proline 82.7617 91.8553 90.8409 359.3972 338.1663 344.0594 67.9805 57.6340 57.9749 118.8846 144.4926 117.2358 Serine 220.4652 251.8763 230.9355 202.7734 203.0658 205.8240 Threonine 388.4981 434.5581 405.0570 302.6392 350.2393 287.6696 Tryptophan 12.4508 15.2310 11.2522 10.7284 10.8762 10.0154 Tyrosine 65.5446 71.2255 60.9647 56.0753 59.8148 54.4807 Valine 93.9793 110.2788 96.4608 70.2507 86.6458 75.4704 MS_METABOLITE_DATA_END #METABOLITES METABOLITES_START metabolite_name moverz_quant ri ri_type pubchem_id inchi_key kegg_id other_id other_id_type Alanine 260.17, 171 4.16 UFLORIDA_MS_RI 5950 C00041 UFLORIDA_FEATURE Arginine 345.21, 170.9 2.68 UFLORIDA_MS_RI 6322 C00062 UFLORIDA_FEATURE Asparagine 303.13, 170.9 2.25 UFLORIDA_MS_RI 6267 C00152 UFLORIDA_FEATURE Aspartic Acid 304.11, 171 2.99 UFLORIDA_MS_RI 5960 C00049 UFLORIDA_FEATURE Citrulline 346.21, 171 3.33 UFLORIDA_MS_RI 9750 C00327 UFLORIDA_FEATURE Glutamic Acid 318.11, 171.1 3.35 UFLORIDA_MS_RI 33032 UFLORIDA_FEATURE Glutamine 317.21, 171 2.65 UFLORIDA_MS_RI 5961 C00064 UFLORIDA_FEATURE Glycine 246.08, 170.9 2.81 UFLORIDA_MS_RI 750 C00037 UFLORIDA_FEATURE Histidine 326.21, 110 2.07 UFLORIDA_MS_RI 6274 C00135 UFLORIDA_FEATURE Isoleucine 302.21, 170.9 8.15 UFLORIDA_MS_RI 6306 C00407 UFLORIDA_FEATURE Leucine 302.21, 170.9 8.26 UFLORIDA_MS_RI 6106 C00123 UFLORIDA_FEATURE Lysine 487.21, 170.9 6.66 UFLORIDA_MS_RI 5962 C00047 UFLORIDA_FEATURE Methionine 320.21, 170.9 6.87 UFLORIDA_MS_RI 6137 C00073 UFLORIDA_FEATURE Ornithine 473.22, 170.9 5.93 UFLORIDA_MS_RI 6262 C00077 UFLORIDA_FEATURE Phenylalanine 336.21, 170.9 8.40 UFLORIDA_MS_RI 6140 C00079 UFLORIDA_FEATURE Proline 286.16, 171 4.84 UFLORIDA_MS_RI 145742 C00148 UFLORIDA_FEATURE Serine 276.11, 170.9 2.60 UFLORIDA_MS_RI 5951 C00065 UFLORIDA_FEATURE Threonine 290.11, 170.9 3.74 UFLORIDA_MS_RI 6288 C00188 UFLORIDA_FEATURE Tryptophan 375.21, 171 8.54 UFLORIDA_MS_RI 6305 C00078 UFLORIDA_FEATURE Tyrosine 352.21, 170.9 6.66 UFLORIDA_MS_RI 6057 C00082 UFLORIDA_FEATURE Valine 288.21, 171 7.09 UFLORIDA_MS_RI 6287 C00183 UFLORIDA_FEATURE METABOLITES_END #END