#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