#METABOLOMICS WORKBENCH pramodwangikar_20190507_010552 DATATRACK_ID:1721 STUDY_ID:ST001180 ANALYSIS_ID:AN001958 PROJECT_ID:PR000792
VERSION             	1
CREATED_ON             	May 8, 2019, 9:50 am
#PROJECT
PR:PROJECT_TITLE                 	Metabolome Analysis of Synechococcus elongatus PCC 11802
PR:PROJECT_TYPE                  	Metabolomics
PR:PROJECT_SUMMARY               	Metabolomics Analysis of a novel freshwater cyanobacterium, Synechococcus
PR:PROJECT_SUMMARY               	elongatus PCC 11802 isolated by us from Powai Lake, Mumbai, India. PCC 11802
PR:PROJECT_SUMMARY               	cells were grown under ambient and 1% CO2 conditions and metabolomics data was
PR:PROJECT_SUMMARY               	collected in three biological replicates and two technical replicates (n=6). The
PR:PROJECT_SUMMARY               	study aims to find metabolomics changes in this cyanobacterium at elevated CO2
PR:PROJECT_SUMMARY               	levels.
PR:INSTITUTE                     	Indian Institute of Technology-Bombay
PR:DEPARTMENT                    	Department of Chemical Engineering
PR:LABORATORY                    	Biosystems Engineering Lab
PR:LAST_NAME                     	Wangikar
PR:FIRST_NAME                    	Pramod
PR:ADDRESS                       	Room No. 136, Biosystems Engineering Laboratory, Mumbai, Maharashtra, 400076,
PR:ADDRESS                       	India
PR:EMAIL                         	wangikar@iitb.ac.in
PR:PHONE                         	2225764215
PR:FUNDING_SOURCE                	DBT-PAN IIT Center for Bioenergy (Grant No: BT/EB/PAN IIT/2012)
#STUDY
ST:STUDY_TITLE                   	Metabolome Profiling of Synechococcus elogatus PCC 11802
ST:STUDY_TYPE                    	Quantitative Metabolomics
ST:STUDY_SUMMARY                 	Metabolomics Analysis of a novel freshwater cyanobacterium, Synechococcus
ST:STUDY_SUMMARY                 	elongatus PCC 11802 isolated by us from Powai Lake, Mumbai, India. PCC 11802
ST:STUDY_SUMMARY                 	cells were grown under ambient and 1% CO2 conditions and metabolomics data was
ST:STUDY_SUMMARY                 	collected in three biological replicates and two technical replicates (n=6). The
ST:STUDY_SUMMARY                 	study aims to find metabolomics changes in this cyanobacterium at elevated CO2
ST:STUDY_SUMMARY                 	levels.
ST:INSTITUTE                     	Indian Institute of Technology Bombay
ST:DEPARTMENT                    	Department of Chemical Engineering
ST:LABORATORY                    	Biosystems Engineering Lab
ST:LAST_NAME                     	Wangikar
ST:FIRST_NAME                    	Pramod P
ST:ADDRESS                       	Powai
ST:EMAIL                         	wangikar@iitb.ac.in
ST:PHONE                         	+91 (22) 2576 7232
#SUBJECT
SU:SUBJECT_TYPE                  	Bacteria
SU:SUBJECT_SPECIES               	Synechococcus elongatus PCC 11802
SU:TAXONOMY_ID                   	1131
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	PCC 11802 AMBIENT CO2 R1	Conditions:Ambient CO2	
SUBJECT_SAMPLE_FACTORS           	-	PCC 11802 AMBIENT CO2 R2	Conditions:Ambient CO2	
SUBJECT_SAMPLE_FACTORS           	-	PCC 11802 AMBIENT CO2 R3	Conditions:Ambient CO2	
SUBJECT_SAMPLE_FACTORS           	-	PCC 11802 1 PERCENT CO2 R1	Conditions:1% CO2	
SUBJECT_SAMPLE_FACTORS           	-	PCC 11802 1 PERCENT CO2 R2	Conditions:1% CO2	
SUBJECT_SAMPLE_FACTORS           	-	PCC 11802 1 PERCENT CO2 R3	Conditions:1% CO2	
#COLLECTION
CO:COLLECTION_SUMMARY            	The PCC 11802 was grown under ambient and 1% CO2 conditions in triplicates in
CO:COLLECTION_SUMMARY            	shake flasks at 200 uE light intensity, 38 degrees C temperature, 120 rpm. The
CO:COLLECTION_SUMMARY            	samples were collected in exponential phase (OD730 = 0.6).The metabolites were
CO:COLLECTION_SUMMARY            	extracted using methanol-chloroform-water method as described in "Metabolite
CO:COLLECTION_SUMMARY            	Extraction Protocol" file. The samples were stored in a -80 degrees C deep
CO:COLLECTION_SUMMARY            	freezer until analyzed using LCMS.
CO:SAMPLE_TYPE                   	Cultured cells
#TREATMENT
TR:TREATMENT_SUMMARY             	The metabolites were extracted using a methanol-chloroform-water method
TR:TREATMENT_SUMMARY             	described in the "Metabolite Extraction" file of the collection data.
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	The metabolite extracts of different collected samples were reconstituted in 100
SP:SAMPLEPREP_SUMMARY            	μL of 50/50 methanol-water mixture. An equal amount of fully 13C-labeled
SP:SAMPLEPREP_SUMMARY            	biomass extract from cyanobacterium Synechococcus elongatus PCC 11801 was added
SP:SAMPLEPREP_SUMMARY            	as internal standard. The mixture is vortexed. The samples are filtered through
SP:SAMPLEPREP_SUMMARY            	syringe filters. Injection volume was 6 uL.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Shimadzu 20AD
CH:COLUMN_NAME                   	Phenomenex Synergi Hydro RP 100 A (100 x 2mm, 2.5um)
CH:FLOW_GRADIENT                 	0% B (0 min), 0% B (2min), 35% B (8 min), 35% B (10.5 min), 90% B (15.50 min),
CH:FLOW_GRADIENT                 	90% B (20.5 min) and 0% B (22 min)
CH:FLOW_RATE                     	0.3 mL/minute
CH:SOLVENT_A                     	10 mM tributylamine + 15mM acetic acid in water
CH:SOLVENT_B                     	100% Methanol
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
AN:LABORATORY_NAME               	Biosystems Engineering Lab
AN:OPERATOR_NAME                 	Damini Jaiswal
AN:SOFTWARE_VERSION              	Analyst
#MS
MS:INSTRUMENT_NAME               	ABI Sciex 5600+ TripleTOF
MS:INSTRUMENT_TYPE               	QTOF
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	Data Acquisition was done using IDA method with MS/MS trigerred for top 10
MS:MS_COMMENTS                   	abundant precursor ions. Cycle time = 1s
MS:COLLISION_ENERGY              	-30
MS:ION_SOURCE_TEMPERATURE        	450
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	Area Ratio
MS_METABOLITE_DATA_START
Samples	PCC 11802 AMBIENT CO2 R1	PCC 11802 AMBIENT CO2 R1	PCC 11802 AMBIENT CO2 R2	PCC 11802 AMBIENT CO2 R2	PCC 11802 AMBIENT CO2 R3	PCC 11802 AMBIENT CO2 R3	PCC 11802 1 PERCENT CO2 R1	PCC 11802 1 PERCENT CO2 R1	PCC 11802 1 PERCENT CO2 R2	PCC 11802 1 PERCENT CO2 R2	PCC 11802 1 PERCENT CO2 R3	PCC 11802 1 PERCENT CO2 R3
Factors	Conditions:Ambient CO2	Conditions:Ambient CO2	Conditions:Ambient CO2	Conditions:Ambient CO2	Conditions:Ambient CO2	Conditions:Ambient CO2	Conditions:1% CO2	Conditions:1% CO2	Conditions:1% CO2	Conditions:1% CO2	Conditions:1% CO2	Conditions:1% CO2
3-phosphoglyceric acid	0.8226	0.8134	0.9449	0.9358	0.8654	0.9137	1.695	1.702	0.863	0.8486	1.35	1.387
Fructose 1,6 bisphosphate	0.793	0.7992	0.7864	0.7365	0.8006	0.7609	2.345	2.438	1.71	1.476	1.885	2.105
Fructose-6-phosphate	0.4519	0.3863	0.5698	0.6851	0.7438	0.7478	2.253	2.364	1.635	1.626	2.497	2.45
Glucose-6-phosphate	0.4184	0.4322	0.6088	0.5329	0.6352	0.5702	2.031	2.048	1.537	1.33	2.347	2.407
Sedoheptulose 1,7 bisphosphate	0.00367	0.01864	0.01816	0.02794	0.02016	0.006	0.1246	0.1035	0.09343	0.1004	0.1376	0.1534
Sedoheptulose-7-phosphate	0.5494	0.5644	0.7189	0.7299	0.7159	0.7973	2.009	1.982	1.38	1.374	2.301	2.341
Ribulose 1,5 bisphosphate	0.759	0.8297	1.283	1.348	1.856	1.682	1.272	1.249	0.6306	0.5965	1.045	1.07
Glycerol-3-phosphate	2.993	3.783	3.348	4.093	3.123	2.894	2.496	1.706	1.253	1.688	2.65	2.893
ADP-glucose	11.29	16.72	14.91	17.64	17.84	17.47	8.701	11.7	9.58	12.94	17.74	18.9
UDP-glucose	2.371	2.334	2.731	3.762	3.764	3.801	6.06	4.957	4.427	5.088	6.087	6.955
Phosphoenolpyruvic acid	1.137	1.076	1.197	1.138	0.9881	0.8846	1.23	1.195	0.4488	0.5165	0.7523	0.7199
Acetyl Coenzyme A	26.73	31.34	19.68	31.55	30.14	28.39	18.99	23.59	14.39	23.74	26.86	14.08
Aspartic acid	0.4578	0.6391	0.5844	0.7933	0.6114	0.8224	1.784	2.097	0.9002	1.102	1.38	1.64
Glutamic acid	0.8688	0.8876	1.069	1.069	1.108	1.14	1.278	1.283	1.123	1.147	1.642	1.664
Glutamine	0.8386	0.8171	0.9045	0.9241	1.2	1.179	1.279	1.32	0.8459	0.9202	1.187	1.384
Succinic acid	3.192	3.053	2.624	3.417	1.853	3.047	3.457	5.766	2.108	4.379	2.376	3.238
Sucrose-6-phosphate	0.1991	0.2191	0.1948	0.1712	0.285	0.3103	2.869	2.965	4.12	4.113	6.137	6.686
Sucrose	0.2507	0.2779	0.2652	0.2505	0.465	0.5216	1.088	0.9409	1.633	1.553	1.856	1.914
ATP	1.306	1.368	1.305	1.277	1.469	1.453	2.397	2.415	1.408	1.415	2.222	2.197
ADP	1.341	1.373	1.25	1.386	1.431	1.433	2.424	2.408	1.336	1.381	2.108	2.057
AMP	1.071	1.074	1.581	1.634	1.61	1.634	2.921	3.077	2.677	2.696	3.513	3.629
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	quantified m/z	KEGG ID
3-phosphoglyceric acid	184.98	C00197
Fructose 1,6 bisphosphate	338.96	C05378
Fructose-6-phosphate	259.02	C00085 
Glucose-6-phosphate	259.02	C00668  
Sedoheptulose 1,7 bisphosphate	369.01	C00447 
Sedoheptulose-7-phosphate	289.03	C05382 
Ribulose 1,5 bisphosphate	308.97	C01182 
Glycerol-3-phosphate	171	C00093
ADP-glucose	588.07	C00498
UDP-glucose	565.05	C00029
Phosphoenolpyruvic acid	166.97	C00074
Acetyl Coenzyme A	808.12	C00024
Aspartic acid	132.03	C00049
Glutamic acid	146.04	C00025
Glutamine	145.08	C00064
Succinic acid	117.02	C00042
Sucrose-6-phosphate	421.07	C16688
Sucrose	341.11	C00089  
ATP	505.98	C00002
ADP	426.02	C00008
AMP	346.05	C00020
METABOLITES_END
#END