#METABOLOMICS WORKBENCH nsuhasj_20230625_185514 DATATRACK_ID:4112 STUDY_ID:ST002743 ANALYSIS_ID:AN004447 PROJECT_ID:PR001708
VERSION             	1
CREATED_ON             	June 26, 2023, 10:29 am
#PROJECT
PR:PROJECT_TITLE                 	Metabolomics comparison of lung fibroblasts from Pteropus alecto and Homo
PR:PROJECT_TITLE                 	sapiens
PR:PROJECT_TYPE                  	MS quantitative analysis
PR:PROJECT_SUMMARY               	Targeted Metabolomics was performed to identify differences in central carbon
PR:PROJECT_SUMMARY               	metabolism between lung fibroblasts from black flying fox fruit bat Pteropus
PR:PROJECT_SUMMARY               	alecto (PaLung cells) and Humans (WI-38 cells).
PR:INSTITUTE                     	Duke-NUS Medical School
PR:LAST_NAME                     	Jagannathan
PR:FIRST_NAME                    	Narendra Suhas
PR:ADDRESS                       	Centre for Computational Biology, 8 College Road, Singapore, Singapore, 169857,
PR:ADDRESS                       	Singapore
PR:EMAIL                         	gmsnsja@nus.edu.sg
PR:PHONE                         	(65) 66015073
PR:PROJECT_COMMENTS              	Metabolomics was performed by commissioning to Human Metabolome Technologies
PR:PROJECT_COMMENTS              	(HMT) service.
PR:CONTRIBUTORS                  	Javier Yu Peng Koh, Yoko Itahana, Koji Itahana, Lisa Tucker-Kellogg
#STUDY
ST:STUDY_TITLE                   	Metabolomics comparison of lung fibroblasts from Pteropus alecto and Homo
ST:STUDY_TITLE                   	sapiens
ST:STUDY_TYPE                    	MS Quantitative analysis
ST:STUDY_SUMMARY                 	Targeted Metabolomics was performed to identify differences in central carbon
ST:STUDY_SUMMARY                 	metabolism between lung fibroblasts from black flying fox fruit bat Pteropus
ST:STUDY_SUMMARY                 	alecto (PaLung cells) and Humans (WI-38 cells). For both PaLung and WI-38 cells,
ST:STUDY_SUMMARY                 	metabolomics measurements were carried out for n = 3 biological replicates.
ST:INSTITUTE                     	Duke-NUS Medical School
ST:LAST_NAME                     	Jagannathan
ST:FIRST_NAME                    	Narendra Suhas
ST:ADDRESS                       	8 College Road, Singapore, Singapore, 169857, Singapore
ST:EMAIL                         	gmsnsja@nus.edu.sg
ST:PHONE                         	(65) 66015073
#SUBJECT
SU:SUBJECT_TYPE                  	Cultured cells
SU:SUBJECT_SPECIES               	Pteropus alecto / Homo sapiens
#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           	-	WI38-1	Genotype:Wild-type | Species:H. sapiens	
SUBJECT_SAMPLE_FACTORS           	-	WI38-2	Genotype:Wild-type | Species:H. sapiens	
SUBJECT_SAMPLE_FACTORS           	-	WI38-3	Genotype:Wild-type | Species:H. sapiens	
SUBJECT_SAMPLE_FACTORS           	-	PaLung-1	Genotype:Wild-type | Species:P. alecto	
SUBJECT_SAMPLE_FACTORS           	-	PaLung-2	Genotype:Wild-type | Species:P. alecto	
SUBJECT_SAMPLE_FACTORS           	-	PaLung-3	Genotype:Wild-type | Species:P. alecto	
#COLLECTION
CO:COLLECTION_SUMMARY            	WI-38 and PaLung cells were seeded in a 100 mm dish and harvested 2 days after
CO:COLLECTION_SUMMARY            	seeding according to the protocol provided by Human Metabolome Technologies (HMT
CO:COLLECTION_SUMMARY            	Japan).
CO:SAMPLE_TYPE                   	Cultured fibroblasts
#TREATMENT
TR:TREATMENT_SUMMARY             	PaLung and WI-38 cells were washed with 5% (w/w) mannitol twice and fixed with
TR:TREATMENT_SUMMARY             	methanol containing the internal standard solution. The internal standard
TR:TREATMENT_SUMMARY             	solution was provided by HMT. Lysates were centrifuged at 2,300 x g for 5 min at
TR:TREATMENT_SUMMARY             	4°C, and supernatants were filtered using the provided filter units by
TR:TREATMENT_SUMMARY             	centrifuging at 9,100 × g for 3 hours at 4 °C. Filtrates were evaporated
TR:TREATMENT_SUMMARY             	by SpeedVac Concentrator SPD1010 (Thermo Fisher Scientific) and submitted to HMT
TR:TREATMENT_SUMMARY             	for analysis. The total cell numbers at the time of harvest were about 1.4 x 107
TR:TREATMENT_SUMMARY             	cells for each cell line. Targeted quantitative analysis was performed by HMT
TR:TREATMENT_SUMMARY             	using capillary electrophoresis mass spectrometry (CE-TOFMS and CE-QqQMS).
TR:TREATMENT_SUMMARY             	Absolute abundances (normalized by cell numbers) were obtained for a total of
TR:TREATMENT_SUMMARY             	116 metabolites (54 and 62 metabolites in the cation and anion modes,
TR:TREATMENT_SUMMARY             	respectively).
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	PaLung and WI-38 cells were washed with 5% (w/w) mannitol twice and fixed with
SP:SAMPLEPREP_SUMMARY            	methanol containing the internal standard solution. The internal standard
SP:SAMPLEPREP_SUMMARY            	solution was provided by HMT. Lysates were centrifuged at 2,300 x g for 5 min at
SP:SAMPLEPREP_SUMMARY            	4°C, and supernatants were filtered using the provided filter units by
SP:SAMPLEPREP_SUMMARY            	centrifuging at 9,100 × g for 3 hours at 4 °C. Filtrates were evaporated
SP:SAMPLEPREP_SUMMARY            	by SpeedVac Concentrator SPD1010 (Thermo Fisher Scientific) and submitted to HMT
SP:SAMPLEPREP_SUMMARY            	for analysis. The total cell numbers at the time of harvest were about 1.4 x 107
SP:SAMPLEPREP_SUMMARY            	cells for each cell line. Targeted quantitative analysis was performed by HMT
SP:SAMPLEPREP_SUMMARY            	using capillary electrophoresis mass spectrometry (CE-TOFMS and CE-QqQMS).
SP:SAMPLEPREP_SUMMARY            	Absolute abundances (normalized by cell numbers) were obtained for a total of
SP:SAMPLEPREP_SUMMARY            	116 metabolites (54 and 62 metabolites in the cation and anion modes,
SP:SAMPLEPREP_SUMMARY            	respectively).
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	CE
CH:INSTRUMENT_NAME               	Agilent CE
CH:COLUMN_NAME                   	Fused silica capillary, i.d. 50 μm × 80 cm
CH:SOLVENT_A                     	NA
CH:SOLVENT_B                     	NA
CH:FLOW_GRADIENT                 	NA
CH:FLOW_RATE                     	NA
CH:COLUMN_TEMPERATURE            	NA
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Agilent CE-TOFMS
MS:INSTRUMENT_TYPE               	Other
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	Peaks detected in CE-TOFMS analysis were extracted using automatic integration
MS:MS_COMMENTS                   	software (MasterHands ver.2.18.0.1 developed at Keio University) (4) and those
MS:MS_COMMENTS                   	in CE-QqQMS analysis were extracted using automatic integration software
MS:MS_COMMENTS                   	(MassHunter Quantitative Analysis B.06.00 Agilent Technologies, Santa Clara, CA,
MS:MS_COMMENTS                   	USA) in order to obtain peak information, which includes m/z, migration time
MS:MS_COMMENTS                   	(MT), and peak area.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	pmol/10^6 cells
MS_METABOLITE_DATA_START
Samples	WI38-1	WI38-2	WI38-3	PaLung-1	PaLung-2	PaLung-3
Factors	Genotype:Wild-type | Species:H. sapiens	Genotype:Wild-type | Species:H. sapiens	Genotype:Wild-type | Species:H. sapiens	Genotype:Wild-type | Species:P. alecto	Genotype:Wild-type | Species:P. alecto	Genotype:Wild-type | Species:P. alecto
Urea	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Gly	24307.2	22607.3	21737.1	9857.7	10531.9	10572.5
Putrescine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Ala	41203.7	38676.5	40866.5	11938.4	11644.3	11543.4
Beta-Ala	422.1	428.3	423.1	1977.6	1877.6	2113.9
Sarcosine	224.5	129.5	209.1	N.D.	N.D.	N.D.
N,N-Dimethylglycine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Gamma-Aminobutyric acid	250.0	238.6	274.4	527.0	452.8	468.6
Choline	127.7	90.7	52.5	858.6	842.8	795.2
Ser	41175.2	38109.1	38737.3	13256.0	13219.5	12711.0
Carnosine	N.D.	N.D.	N.D.	1183.7	1137.9	1258.7
Creatinine	227.0	224.2	242.6	456.7	313.9	342.8
Pro	17069.0	16121.9	17025.3	13000.1	11737.3	11132.3
Val	16022.6	14944.9	16280.9	7668.2	6689.5	6315.9
Betaine	429.0	417.3	417.3	N.D.	184.1	187.3
Homoserine	23.6	24.8	24.4	N.D.	N.D.	N.D.
Thr	72006.1	65802.5	65521.4	18867.8	18793.6	17106.3
Betaine aldehyde	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Cys	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Hydroxyproline	1001.8	909.0	940.6	642.2	560.8	571.5
Creatine	3846.0	3768.5	4270.7	22335.2	18029.6	18300.5
Leu	23711.8	23523.0	23828.8	8223.7	8006.9	7463.5
Ile	15459.3	15474.3	15853.3	6871.8	6553.0	6036.0
Asn	973.3	1005.4	1074.4	576.5	476.9	501.9
Ornithine	178.8	185.8	196.4	302.1	253.7	271.2
Asp	15632.0	15511.5	15818.9	3632.8	3454.4	3153.5
Homocysteine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Adenine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Hypoxanthine	N.D.	N.D.	N.D.	253.9	242.1	252.3
Spermidine	68.4	45.1	43.2	N.D.	N.D.	N.D.
Gln	22904.3	22961.9	23511.8	4120.1	3821.3	4147.9
Lys	1550.7	1441.7	1443.2	1061.2	910.5	928.8
Glu	126774.1	124192.7	130893.5	69337.8	67267.4	64394.4
Met	91.7	210.7	74.8	N.D.	N.D.	N.D.
Guanine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
His	8159.1	7417.6	7001.5	2452.4	2272.4	2345.2
Carnitine	47.6	54.7	68.0	213.6	175.1	161.3
Phe	11686.6	10972.6	11209.7	3545.7	3489.9	3340.1
Arg	1192.2	1128.8	1141.6	535.3	433.8	436.1
Citrulline	348.1	353.2	350.7	150.4	114.6	132.3
Tyr	10158.3	9696.5	10487.8	3178.2	3107.7	2833.0
S-Adenosylhomocysteine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Spermine	16.4	N.D.	N.D.	N.D.	N.D.	N.D.
Trp	260.4	287.5	320.8	147.1	N.D.	102.9
Cystathionine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Adenosine	104.7	87.7	99.9	119.9	103.7	116.7
Inosine	N.D.	N.D.	N.D.	N.D.	544.2	649.8
Guanosine	N.D.	N.D.	N.D.	N.D.	N.D.	N.D.
Argininosuccinic acid	83.8	97.7	98.5	N.D.	N.D.	N.D.
Glutathione (GSSG)	3308.3	3245.4	3437.3	4507.3	3799.0	3736.9
Glutathione (GSH)	492.8	475.2	485.8	1029.6	853.6	916.7
S-Adenosylmethionine	187.2	190.9	170.0	181.5	160.3	170.8
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	PubChem ID	HMDB ID
Urea	1176	HMDB0000294
Gly	750	HMDB0000123
Putrescine	1045	HMDB0001414
Ala	602	"HMDB0000161,HMDB0001310"
Beta-Ala	239	HMDB0000056
Sarcosine	1088	HMDB0000271
N,N-Dimethylglycine	673	HMDB0000092
Gamma-Aminobutyric acid	119	HMDB0000112
Choline	305	HMDB0000097
Ser	617	"HMDB0000187,HMDB0003406"
Carnosine	439224	HMDB0000033
Creatinine	588	HMDB0000562
Pro	614	"HMDB0000162,HMDB0003411"
Val	1182	HMDB0000883
Betaine	247	HMDB0000043
Homoserine	12647	HMDB0000719
Thr	6288	HMDB0000167
Betaine aldehyde	249	HMDB0001252
Cys	594	"HMDB0000574,HMDB0003417"
Hydroxyproline	5810	HMDB0000725
Creatine	586	HMDB0000064
Leu	857	HMDB0000687
Ile	791	HMDB0000172
Asn	236	"HMDB0000168,HMDB0033780"
Ornithine	389	"HMDB0000214,HMDB0003374"
Asp	424	"HMDB0000191,HMDB0006483"
Homocysteine	778	HMDB0000742
Adenine	190	HMDB0000034
Hypoxanthine	790	HMDB0000157
Spermidine	1102	HMDB0001257
Gln	738	"HMDB0000641,HMDB0003423"
Lys	866	"HMDB0000182,HMDB0003405"
Glu	611	"HMDB0000148,HMDB0003339"
Met	876	HMDB0000696
Guanine	764	HMDB0000132
His	773	HMDB0000177
Carnitine	85	HMDB0000062
Phe	994	HMDB0000159
Arg	6322	"HMDB0000517,HMDB0003416"
Citrulline	9750	HMDB0000904
Tyr	1153	HMDB0000158
S-Adenosylhomocysteine	439155	HMDB0000939
Spermine	1103	HMDB0001256
Trp	1148	HMDB0000929
Cystathionine	834	HMDB0000099
Adenosine	60961	HMDB0000050
Inosine	6021	HMDB0000195
Guanosine	6802	HMDB0000133
Argininosuccinic acid	16950	HMDB0000052
Glutathione (GSSG)	65359	HMDB0003337
Glutathione (GSH)	124886	HMDB0000125
S-Adenosylmethionine	34755	HMDB0001185
METABOLITES_END
#END