#METABOLOMICS WORKBENCH ankita_pal_20220202_062900_mwtab.txt DATATRACK_ID:3059 STUDY_ID:ST002076 ANALYSIS_ID:AN003384 PROJECT_ID:PR001316
VERSION             	1
CREATED_ON             	February 2, 2022, 1:22 pm
#PROJECT
PR:PROJECT_TITLE                 	Metabolomic analysis of Escherichia coli K-12 MG1655 transcriptional regulator
PR:PROJECT_TITLE                 	double mutants under anaerobic conditions
PR:PROJECT_TYPE                  	Metabolomics
PR:PROJECT_SUMMARY               	Metabolomic analysis of Wildtype, fnr_arcA (FA), arcA_ihf (AI) and fnr_ihf (FI)
PR:PROJECT_SUMMARY               	mutants in glucose minimal media under anaerobic fermentation conditions during
PR:PROJECT_SUMMARY               	its exponential phase of growth. Three biological and two technical replicates
PR:PROJECT_SUMMARY               	samples (n=6) were harvested for each of the strains while growing in a
PR:PROJECT_SUMMARY               	bioreactor anaerobically at 37 degrees Celsius and 150 rpm. This study aims to
PR:PROJECT_SUMMARY               	characterize and compare the metabolic profiles of all these strains.
PR:INSTITUTE                     	IIT Bombay
PR:DEPARTMENT                    	Department of Chemical Engineering
PR:LABORATORY                    	Systems Biology and Metabolic Engineering Laboratory
PR:LAST_NAME                     	Pal
PR:FIRST_NAME                    	Ankita
PR:ADDRESS                       	Department of Chemical Engineering, IIT Bombay, Mumbai, Maharashtra, 400076,
PR:ADDRESS                       	India
PR:EMAIL                         	pal.ankita90@gmail.com
PR:PHONE                         	08879536816
#STUDY
ST:STUDY_TITLE                   	Metabolomic study of Escherichia coli K-12 MG1655 WT and its transcriptional
ST:STUDY_TITLE                   	regulator double mutants under anaerobic fermentation conditions
ST:STUDY_TYPE                    	Metabolomics
ST:STUDY_SUMMARY                 	Metabolomic analysis of Wildtype, fnr_arcA (FA), arcA_ihf (AI) and fnr_ihf (FI)
ST:STUDY_SUMMARY                 	mutants in glucose minimal media under anaerobic fermentation conditions during
ST:STUDY_SUMMARY                 	its exponential phase of growth. Three biological and two technical replicate
ST:STUDY_SUMMARY                 	samples (n=6) were harvested for each of the strains while growing in a
ST:STUDY_SUMMARY                 	bioreactor anaerobically at 37 degrees Celsius and 150 rpm. This study aims to
ST:STUDY_SUMMARY                 	characterize and compare the metabolic profiles of all these strains.
ST:INSTITUTE                     	IIT Bombay
ST:DEPARTMENT                    	Department of Chemical Engineering
ST:LABORATORY                    	Systems Biology and Metabolic Engineering Laboratory (SBMEL)
ST:LAST_NAME                     	Pal
ST:FIRST_NAME                    	Ankita
ST:ADDRESS                       	Department of Chemical Engineering, IIT Bombay, Mumbai, Maharashtra, 400076,
ST:ADDRESS                       	India
ST:EMAIL                         	pal.ankita90@gmail.com
ST:PHONE                         	08879536816
#SUBJECT
SU:SUBJECT_TYPE                  	Bacteria
SU:SUBJECT_SPECIES               	Escherichia coli
SU:TAXONOMY_ID                   	562
SU:GENOTYPE_STRAIN               	K-12 MG1655
#FACTORS
#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           	Wild-type_1	WT_1	Genotype:Wildtype | KO Type:Wildtype	RAW_FILE_NAME=WT_positive_1.RAW;WT_negative_1.RAW
SUBJECT_SAMPLE_FACTORS           	Wild-type_2	WT_2	Genotype:Wildtype | KO Type:Wildtype	RAW_FILE_NAME=WT_positive_2.RAW;WT_negative_2.RAW
SUBJECT_SAMPLE_FACTORS           	Wild-type_3	WT_3	Genotype:Wildtype | KO Type:Wildtype	RAW_FILE_NAME=WT_positive_3.RAW;WT_negative_3.RAW
SUBJECT_SAMPLE_FACTORS           	Wild-type_4	WT_4	Genotype:Wildtype | KO Type:Wildtype	RAW_FILE_NAME=WT_positive_4.RAW;WT_negative_4.RAW
SUBJECT_SAMPLE_FACTORS           	Wild-type_5	WT_5	Genotype:Wildtype | KO Type:Wildtype	RAW_FILE_NAME=WT_positive_5.RAW;WT_negative_5.RAW
SUBJECT_SAMPLE_FACTORS           	Wild-type_6	WT_6	Genotype:Wildtype | KO Type:Wildtype	RAW_FILE_NAME=WT_positive_6.RAW;WT_negative_6.RAW
SUBJECT_SAMPLE_FACTORS           	FA-knockout_1	FA_1	Genotype:Mutant | KO Type:FA	RAW_FILE_NAME=FA_positive_1.RAW;FA_negative_1.RAW
SUBJECT_SAMPLE_FACTORS           	FA-knockout_2	FA_2	Genotype:Mutant | KO Type:FA	RAW_FILE_NAME=FA_positive_2.RAW;FA_negative_2.RAW
SUBJECT_SAMPLE_FACTORS           	FA-knockout_3	FA_3	Genotype:Mutant | KO Type:FA	RAW_FILE_NAME=FA_positive_3.RAW;FA_negative_3.RAW
SUBJECT_SAMPLE_FACTORS           	FA-knockout_4	FA_4	Genotype:Mutant | KO Type:FA	RAW_FILE_NAME=FA_positive_4.RAW;FA_negative_4.RAW
SUBJECT_SAMPLE_FACTORS           	FA-knockout_5	FA_5	Genotype:Mutant | KO Type:FA	RAW_FILE_NAME=FA_positive_5.RAW;FA_negative_5.RAW
SUBJECT_SAMPLE_FACTORS           	FA-knockout_6	FA_6	Genotype:Mutant | KO Type:FA	RAW_FILE_NAME=FA_positive_6.RAW;FA_negative_6.RAW
SUBJECT_SAMPLE_FACTORS           	AI-knockout_1	AI_1	Genotype:Mutant | KO Type:AI	RAW_FILE_NAME=AI_positive_1.RAW;AI_negative_1.RAW
SUBJECT_SAMPLE_FACTORS           	AI-knockout_2	AI_2	Genotype:Mutant | KO Type:AI	RAW_FILE_NAME=AI_positive_2.RAW;AI_negative_2.RAW
SUBJECT_SAMPLE_FACTORS           	AI-knockout_3	AI_3	Genotype:Mutant | KO Type:AI	RAW_FILE_NAME=AI_positive_3.RAW;AI_negative_3.RAW
SUBJECT_SAMPLE_FACTORS           	AI-knockout_4	AI_4	Genotype:Mutant | KO Type:AI	RAW_FILE_NAME=AI_positive_4.RAW;AI_negative_4.RAW
SUBJECT_SAMPLE_FACTORS           	AI-knockout_5	AI_5	Genotype:Mutant | KO Type:AI	RAW_FILE_NAME=AI_positive_5.RAW;AI_negative_5.RAW
SUBJECT_SAMPLE_FACTORS           	AI-knockout_6	AI_6	Genotype:Mutant | KO Type:AI	RAW_FILE_NAME=AI_positive_6.RAW;AI_negative_6.RAW
SUBJECT_SAMPLE_FACTORS           	FI-knockout_1	FI_1	Genotype:Mutant | KO Type:FI	RAW_FILE_NAME=FI_positive_1.RAW;FI_negative_1.RAW
SUBJECT_SAMPLE_FACTORS           	FI-knockout_2	FI_2	Genotype:Mutant | KO Type:FI	RAW_FILE_NAME=FI_positive_2.RAW;FI_negative_2.RAW
SUBJECT_SAMPLE_FACTORS           	FI-knockout_3	FI_3	Genotype:Mutant | KO Type:FI	RAW_FILE_NAME=FI_positive_3.RAW;FI_negative_3.RAW
SUBJECT_SAMPLE_FACTORS           	FI-knockout_4	FI_4	Genotype:Mutant | KO Type:FI	RAW_FILE_NAME=FI_positive_4.RAW;FI_negative_4.RAW
SUBJECT_SAMPLE_FACTORS           	FI-knockout_5	FI_5	Genotype:Mutant | KO Type:FI	RAW_FILE_NAME=FI_positive_5.RAW;FI_negative_5.RAW
SUBJECT_SAMPLE_FACTORS           	FI-knockout_6	FI_6	Genotype:Mutant | KO Type:FI	RAW_FILE_NAME=FI_positive_6.RAW;FI_negative_6.RAW
#COLLECTION
CO:COLLECTION_SUMMARY            	The WT, FA, AI and FI mutants were grown in a bioreactor in glucose minimal
CO:COLLECTION_SUMMARY            	media under anaerobic fermentation conditions at 37 degrees Celsius and 150 rpm.
CO:COLLECTION_SUMMARY            	The samples were harvested during its exponential phase of growth for three
CO:COLLECTION_SUMMARY            	biological and two technical replicates (n=6). The metabolites were extracted
CO:COLLECTION_SUMMARY            	using the Methanol-Chloroform-Water method. Detailed sample collection protocol
CO:COLLECTION_SUMMARY            	is described in “Extraction_protocol_msi.pdf”.
CO:COLLECTION_PROTOCOL_FILENAME  	Extraction_protocol_msi.pdf
CO:SAMPLE_TYPE                   	Bacterial cells
CO:COLLECTION_METHOD             	Methanol-Chloroform-Water method
CO:COLLECTION_LOCATION           	IIT Bombay, Powai, Mumbai- 400076, Mumbai, Maharashtra
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	The WT, FA, AI and FI mutants were grown in a bioreactor in glucose minimal
TR:TREATMENT_SUMMARY             	media under anaerobic fermentation conditions at 37 degrees Celsius and 150 rpm.
TR:TREATMENT_SUMMARY             	The samples were harvested during its exponential phase of growth for three
TR:TREATMENT_SUMMARY             	biological and two technical replicates (n=6). The metabolites were extracted
TR:TREATMENT_SUMMARY             	using the Methanol-Chloroform-Water method.
TR:CELL_GROWTH_CONTAINER         	Bioreactor
TR:CELL_MEDIA                    	M9 + Glucose
TR:CELL_ENVIR_COND               	37 degrees Celsius, 150 rpm. anaerobic fermentation
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Samples were extracted from the Wildtype, FA, AI and FI mutants grown in a
SP:SAMPLEPREP_SUMMARY            	bioreactor anaerobically in glucose minimal media at 37 degrees Celsius and 150
SP:SAMPLEPREP_SUMMARY            	rpm. The metabolites were extracted using the Methanol-Chloroform-Water method.
SP:SAMPLEPREP_SUMMARY            	The samples were spiked with an equal volume of 13C-labelled internal standard
SP:SAMPLEPREP_SUMMARY            	taken from the same batch at an earlier stage to prevent to account for losses
SP:SAMPLEPREP_SUMMARY            	due to metabolite degradation and to enable robust quantification circumventing
SP:SAMPLEPREP_SUMMARY            	the ion-suppression effects.
SP:SAMPLEPREP_PROTOCOL_FILENAME  	Method_msi.pdf
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	The detailed chromatography and MS protocol has been described in
CH:CHROMATOGRAPHY_SUMMARY        	"Method_msi.pdf" file.
CH:CHROMATOGRAPHY_TYPE           	HILIC
CH:INSTRUMENT_NAME               	Thermo Dionex Ultimate 3000
CH:COLUMN_NAME                   	SeQuant ZIC- pHILIC (150 x 2.1mm, 5um)
CH:METHODS_FILENAME              	Method_msi.pdf
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive Plus Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	Data acquisition done using parent ion MS intensities. Peak height used for
MS:MS_COMMENTS                   	processing. Xcalibur 4.3.73.11 used for data analysis and peak integration.
MS:MS_COMMENTS                   	Missing value imputation was done using SVD impute function in MetaboAnalyst.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	umol/gDCW and Height ratio/gDCW
MS_METABOLITE_DATA_START
Samples	WT_1	WT_2	WT_3	WT_4	WT_5	WT_6	FA_1	FA_2	FA_3	FA_4	FA_5	FA_6	FI_1	FI_2	FI_3	FI_4	FI_5	FI_6	AI_1	AI_2	AI_3	AI_4	AI_5	AI_6
Factors	Genotype:Wildtype | KO Type:Wildtype	Genotype:Wildtype | KO Type:Wildtype	Genotype:Wildtype | KO Type:Wildtype	Genotype:Wildtype | KO Type:Wildtype	Genotype:Wildtype | KO Type:Wildtype	Genotype:Wildtype | KO Type:Wildtype	Genotype:Mutant | KO Type:FA	Genotype:Mutant | KO Type:FA	Genotype:Mutant | KO Type:FA	Genotype:Mutant | KO Type:FA	Genotype:Mutant | KO Type:FA	Genotype:Mutant | KO Type:FA	Genotype:Mutant | KO Type:FI	Genotype:Mutant | KO Type:FI	Genotype:Mutant | KO Type:FI	Genotype:Mutant | KO Type:FI	Genotype:Mutant | KO Type:FI	Genotype:Mutant | KO Type:FI	Genotype:Mutant | KO Type:AI	Genotype:Mutant | KO Type:AI	Genotype:Mutant | KO Type:AI	Genotype:Mutant | KO Type:AI	Genotype:Mutant | KO Type:AI	Genotype:Mutant | KO Type:AI
alpha-Ketoglutarate	2.431658199	1.789205951	2.116091928	2.066433109	2.065677459	2.033558554	0.645455877	0.670380777	0.810876123	0.688494656	0.718399225	0.741767601	5.451844176	4.349768495	3.118201654	6.99356292	3.339051315	3.815928868	2.353047994	2.131632308	1.53433966	2.415531879	2.798605127	1.300210696
Fructose-6-Phosphate	5.423763876	4.405486791	16.3142903	16.01143151	11.56342273	7.43821452	3.548670156	5.097620367	3.226504662	3.34108056	4.437055681	2.943447491	17.14735864	4.304808135	4.06002902	16.95621135	4.24102909	3.412656486	17.70890523	4.740773527	4.351307618	4.158460711	16.65900464	4.52662528
Ribose-5-Phosphate	0.032151329	0.033917529	0.007234757	0.006565163	0.009298473	0.03248734	0.087262281	0.009336461	0.007318936	0.104591166	0.010930377	0.008211962	0.075553007	0.027247941	0.027289401	0.073286812	0.026333036	0.026723389	0.123031421	0.031658902	0.04333407	0.033049069	0.137606392	0.041960035
Malate	19.90638065	21.43032129	73.1064053	74.62490908	70.69678736	36.06239724	34.81226503	41.13542881	57.25997478	34.01959798	41.74953429	40.80929187	289.5362847	66.20505059	68.69375201	214.772623	60.51750289	49.55848354	316.6736039	94.76669124	55.71567261	102.6653924	214.2011088	71.19731941
Glucose-6-Phosphate	13.55050768	14.04397965	29.99861101	30.35839114	26.21402194	19.88002931	9.172061412	12.15652294	9.093103851	9.541828301	12.59363154	8.871851162	40.83291917	8.295110796	4.526320319	40.04789451	8.478892436	4.506587429	42.14467869	9.771357961	9.080480875	9.694708739	38.52490195	9.159506135
Phosphoenolpyruvate	4.798302669	4.894499749	3.255626549	3.303384229	2.099187447	7.255092022	6.957524323	6.779696933	8.594360489	6.955638168	6.638804464	8.60501488	4.777013053	10.976974	15.47544825	4.910222708	10.69721985	15.21845978	5.482889315	19.41841918	17.77764946	19.00523441	5.299408007	17.68766984
ATP	6.535747233	7.088436002	22.66024116	24.79560275	28.08890445	11.8337033	8.821950864	6.976241976	11.49960381	9.001994269	7.115437722	12.36655837	16.26314977	12.13868745	13.9606097	24.73906658	NA	13.4647948	16.829705	21.39663772	15.40383268	22.77940296	40.45357753	15.13112394
Fumarate	4.787772326	5.053553076	14.04159696	11.87665569	12.89083684	10.79603175	4.990073876	7.45749267	11.12538914	4.605361506	7.441668957	1.564585934	41.65672928	6.509451872	10.97478332	23.76191327	6.145993175	10.12031909	103.9344562	25.55038665	23.80622659	18.18004731	8.142778871	8.266179032
ADP	16.33020003	15.82054574	28.08652004	25.79234697	27.85409634	18.47939606	10.90317923	10.96211187	12.63993921	10.61022077	10.34980479	13.56169469	23.2060676	21.54407296	21.05266699	24.18633955	22.20945593	22.10040325	31.44313876	26.5476842	23.89947915	24.16662705	30.62012497	21.02929955
AMP	21.99569867	21.16336754	19.3854082	19.11392645	21.22883989	21.77028447	12.13399228	10.98541526	13.58359569	12.06911331	10.4213231	14.41029447	21.77355095	48.55258893	42.3862744	24.8010042	47.2199083	43.39773111	27.1860819	34.41300661	43.4843683	33.05995754	30.72670448	38.475703
Glycerate-3-phosphate	0.89684201	0.9045242	0.669196109	0.666518854	0.479202265	1.304808282	0.430995807	0.475604684	0.477289952	0.427815192	0.479060106	0.472759317	1.211825136	0.860321196	0.778685213	1.210638705	0.865132558	0.773263862	1.401317563	1.221568162	1.236765663	1.210419807	1.416808944	1.258792542
Citrate	0.766071741	0.757975285	1.480071035	1.464291765	1.834493128	0.81563741	0.260000778	0.229054813	0.339400878	0.259520854	0.226569304	0.34252183	1.943411865	1.308118093	0.652162399	1.978200368	1.323789535	0.786306135	0.99786812	0.551879205	0.481993416	0.562321795	1.039222309	0.472675714
Fructose-1,6-bisphosphate	0.30287192	0.305494968	1.14130549	1.194830878	0.998739348	0.287761915	0.303983467	0.295826768	0.311870051	0.28489005	0.29394869	0.298914464	1.47209977	0.637781753	0.560905165	1.440010955	0.612959607	0.545452751	1.80988431	0.64503778	0.880307706	0.640489168	1.570475143	0.923816763
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	m/z [M-H]-	KEGG-id
alpha-Ketoglutarate	145.0142	C00026
Ribose-5-Phosphate	229.0118	C00117
Fructose-6-Phosphate	259.0224	C00085
Malate	133.0142	C00149
Glucose-6-Phosphate	259.0224	C00092
Phosphoenolpyruvate	166.975	C00074
Citrate	191.0191	C00158
Fructose-1,6-bisphosphate	338.9887	C00354
Glycerate-3-phosphate	184.9856	C00190
AMP	346.0558	C00020
ADP	426.0221	C00008
ATP	505.9885	C00002
Fumarate	115.0036	C00122
METABOLITES_END
#END