#METABOLOMICS WORKBENCH ankita_pal_20220202_062900_mwtab.txt DATATRACK_ID:3059 STUDY_ID:ST002076 ANALYSIS_ID:AN003383 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                      	POSITIVE
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
Leucine	4.339392777	4.071342108	4.596626868	4.595376637	5.52	5.18	1.334135164	1.142967846	1.651358914	1.327865207	1.182408213	1.660768564	13.13477172	9.708554001	7.844353096	13.34449652	9.981734138	8.064252229	8.033331143	6.387733342	4.327148457	6.326741784	7.97885782	4.382174085
Phenylalanine	0.663109999	0.656541175	0.631053559	0.631705113	0.73	0.97	0.249103815	0.211276351	0.304333072	0.24610561	0.375756323	0.313151704	0.956369382	0.413428159	0.450790316	0.943536605	0.415352214	0.463092186	1.039098337	0.460916111	0.32387146	0.456135049	1.06090185	0.327080822
Methionine	1.71898291	1.653582903	1.962846801	2.00167123	1.93	2.15	0.809105347	0.744985835	0.936326646	0.823942542	0.656912025	0.964997275	2.596011115	2.280334375	2.103459035	2.572091412	2.309892442	2.059355598	2.216351743	2.387191458	2.279863547	2.52827834	2.236288269	2.241145615
Tryptophan	0.133562342	0.135524122	0.13148099	0.130893034	0.13	0.2	0.051499636	0.049692294	0.066156015	0.055456579	0.044874762	0.063890949	0.202518088	0.146312025	0.138886819	0.204197166	0.143898154	0.144802108	0.207042205	0.169314626	0.102786818	0.17051645	0.245702228	0.116702147
Proline	0.596864506	0.584915861	1.104842009	1.0868342	1.27	0.88	0.400966594	0.261354198	0.582431191	0.398185198	0.251919237	0.592504798	1.736433064	1.588997552	1.376301542	1.746776693	1.552134071	1.398536279	1.339420586	1.502309697	1.133164846	1.448321534	1.391743901	1.080259513
Valine	5.386763361	3.10520573	5.572423982	5.628870515	8.29	4.63	1.169024584	0.994124749	1.451451436	1.160306247	1.101671581	1.479356255	13.25549206	10.77838939	11.33446195	13.71297705	16.33583116	11.33608115	7.399753537	7.160023033	3.896128804	6.964498972	7.363162506	4.012660142
Tyrosine	1.18408796	1.198604713	1.846440277	1.95226411	2.85	1.6	0.688484691	0.609683335	0.834538669	0.674679286	0.844092749	0.815284925	2.05756395	1.341043262	1.607711998	2.18447674	1.305745163	1.483789946	1.966238912	1.24833081	0.868799448	1.268291745	1.849540016	0.878637368
Alanine	23.53978108	23.7608482	39.23017769	38.38480395	44.64	33.01	11.09705196	14.40442051	10.215565	11.33743009	32.006788	10.27019811	51.35264341	29.33835716	29.15341321	55.25011896	30.60755955	30.27611738	36.96062397	24.01924677	16.48727101	23.03208426	37.45738569	17.32539386
Threonine	2.163773106	2.197844239	2.695540594	2.679859374	3.31	2.69	1.003416315	0.774235989	1.337012406	1.020482931	0.523302155	1.318657568	7.352846629	8.476907083	8.109597865	7.555817018	8.923354349	7.814753122	4.314708604	5.015911955	4.209758247	5.287019882	3.968316975	4.238999661
Histidine	0.6430585	0.642164429	0.976755049	1.091947178	1.244768712	0.887764829	0.480039502	0.445725835	0.604561256	0.472007288	0.424618584	0.624710337	1.27	0.98	1.02	NA	NA	0.773012391	1.283088491	1.106460705	0.824720654	1.048230798	1.386763257	0.71822009
Glutamine	0.463601549	0.436838633	1.580567461	1.56681558	2.83	0.68	1.198375254	0.531566011	1.946179442	1.123691571	0.4027878	1.932088688	4.123833534	5.219206702	2.256411571	4.500606506	5.491305112	2.263248441	3.839001618	5.426154434	4.986428622	5.289201944	3.805365794	5.100114458
Glycine	8.471052718	8.242268544	8.885631666	9.200894163	9.36	11.86	5.672243972	6.134059287	5.808904945	5.449977698	6.243765901	5.944720401	12.60362145	10.13031634	9.944715887	11.99349803	11.45830145	10.15562456	9.587720086	9.134640886	7.61795928	9.183586026	9.774123118	8.030632387
Serine	3.931485656	3.983659613	5.702612629	6.113026786	6.52247969	5.951601445	3.771216435	3.300305058	4.556059306	3.633197807	3.281372259	4.235544666	7.034895717	6.07731881	5.275624112	5.995693538	5.996232873	5.112533214	10.39618612	11.45672079	7.236180924	11.87117691	10.55521518	7.467889646
Asparagine	0.080912663	0.08028805	1.084927517	0.872941862	1.272963641	0.076990564	0.596646647	0.519423728	0.702530706	0.600692996	0.365497949	0.583284478	1.051949844	1.413520058	0.759372982	1.187664172	1.42657615	0.917921429	3.032687323	0.945376282	0.696285242	0.963146153	3.026555421	0.668639426
Glutamate	35.38984382	35.4371323	47.65926338	47.16255016	56.90088362	42.83083614	40.7892424	30.10862297	52.11396594	40.40062771	28.39434272	51.1250243	180.2213361	166.8578447	127.6251226	217.0593375	176.4325318	136.9200022	215.4303849	199.3880864	139.048606	190.0676802	221.0248281	134.7082602
Aspartate	1.668348702	1.773337413	1.830172242	1.544621655	2.142711546	3.311893117	2.46995608	1.863674066	3.015723455	2.369954652	1.113196337	2.962233157	2.735995272	4.403985356	2.196360864	2.892779605	4.587577196	2.24477211	4.441363884	11.8722842	10.75836206	11.20449343	4.346266355	10.605516
Lysine	15.17728428	15.61512655	15.987123	16.22565965	19.81823988	19.95298073	7.315249483	5.909528117	9.543245747	7.227878962	5.718945131	9.51607613	27.17537491	22.94924859	21.23205314	24.43770328	21.74872394	20.05510147	23.03475856	21.4520317	17.07263614	21.4625641	23.09324813	16.41024413
Arginine	3.201064274	3.190855187	2.570239548	2.567657062	2.856752366	4.017516151	2.123937379	1.771744333	2.80122412	2.156409808	1.321718957	2.811148258	4.915660066	4.985660664	4.063997742	4.935120258	4.931470521	4.065967409	4.372042981	4.977456362	3.710968633	5.040338104	4.162525434	3.717987974
NAD	14.50534375	14.33103254	14.97360937	14.64225697	15.23587052	16.65680255	7.38447865	6.767811734	9.359049145	7.332635571	6.639439134	9.409666066	18.75345166	17.02690229	17.60288283	19.64725485	17.53289881	18.15669169	16.93406411	17.26679837	15.03060162	17.3199791	17.03085487	15.31096649
NADPH	0.523640271	0.492833858	0.625037778	0.651290537	0.797642476	0.739486511	0.369522508	0.322234406	0.45185508	0.370111796	0.10526293	0.452310503	0.691723737	0.550166881	0.594680257	NA	NA	NA	0.586918908	0.513756159	0.445295753	0.49843337	0.574081836	0.406857981
GABA	0.040205062	0.0446408	0.045472766	0.030308431	0.030026763	0.036162541	0.091145917	0.08278234	0.120162407	0.091828658	0.092596741	0.11538322	0.784288432	0.514689284	0.482440582	0.806118323	0.508669526	0.45019188	0.374969422	0.206166245	0.143975601	0.205740282	0.380080982	0.149087161
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	m/z [M+H]+	KEGG-id
Leucine	132.1019	C00123
Phenylalanine	166.0862	C00079
Methionine	150.0583	C00073
Tryptophan	205.0971	C00078
Proline	116.0706	C00148
Valine	118.0862	C00183
Tyrosine	182.0811	C00082
Alanine	90.0549	C00041
Threonine	120.0655	C00188
Glutamine	147.0764	C00064
Glycine	76.0393	C00037
Aspartate	134.0447	C00049
Asparagine	133.0607	C00152
Serine	106.0498	C00065
Glutamate	148.0604	C00025
Lysine	147.1128	C00047
Arginine	175.1189	C00062
Histidine	156.0767	C00135
NAD	664.1163	C00003
NADPH	746.0983	C00005
GABA	104.0706	C00334
METABOLITES_END
#END