#METABOLOMICS WORKBENCH nchorna_20201107_014553 DATATRACK_ID:2232 STUDY_ID:ST001612 ANALYSIS_ID:AN002647 PROJECT_ID:000000
VERSION             	1
CREATED_ON             	November 30, 2020, 1:49 pm
#PROJECT
PR:PROJECT_TITLE                 	Comparative metabolomics analysis of two Saccharomyces cerevisiae strains: the
PR:PROJECT_TITLE                 	wild type and mtl1Δ, which carries a deletion of the mechanosensor Mtl1p
PR:PROJECT_SUMMARY               	To gather more in-depth knowledge of the Mtl1p mechanosensor's role in
PR:PROJECT_SUMMARY               	Saccharomyces cerevisiae metabolism, we conducted a comparative metabolomic
PR:PROJECT_SUMMARY               	analysis of two Saccharomyces cerevisiae strains: the wild type and mtl1Δ,
PR:PROJECT_SUMMARY               	which carries a deletion of the mechanosensor Mtl1p. Both strains were grown
PR:PROJECT_SUMMARY               	under normal conditions at 27°C. The most significant metabolic changes between
PR:PROJECT_SUMMARY               	these strains were related to amino acid metabolism, purine metabolism, and
PR:PROJECT_SUMMARY               	carboxylic acid metabolism.
PR:INSTITUTE                     	University of Puerto Rico, Medical Sciences Campus
PR:DEPARTMENT                    	Biochemistry
PR:LAST_NAME                     	Chorna
PR:FIRST_NAME                    	Nataliya
PR:ADDRESS                       	University of Puerto Rico, Medical Sciences Campus, Department of Biochemistry,
PR:ADDRESS                       	Main Building, 6th Floor, Room A-632, San Juan, PR 00935
PR:EMAIL                         	nataliya.chorna@upr.edu
PR:PHONE                         	787-758-2525 ext 1640
PR:FUNDING_SOURCE                	NIGMS-NIH-PRINBRE-P20GM103475
PR:CONTRIBUTORS                  	Nelson Martínez–Matías, Sahily González–Crespo
#STUDY
ST:STUDY_TITLE                   	Comparative metabolomics analysis of two Saccharomyces cerevisiae strains: the
ST:STUDY_TITLE                   	wild type and mtl1Δ, which carries a deletion of the mechanosensor Mtl1p
ST:STUDY_TITLE                   	(part-II)
ST:STUDY_SUMMARY                 	To gather more in-depth knowledge of the Mtl1p mechanosensor's role in
ST:STUDY_SUMMARY                 	Saccharomyces cerevisiae metabolism, we conducted a comparative metabolomic
ST:STUDY_SUMMARY                 	analysis of two Saccharomyces cerevisiae strains: the wild type and mtl1Δ,
ST:STUDY_SUMMARY                 	which carries a deletion of the mechanosensor Mtl1p. Both strains were grown
ST:STUDY_SUMMARY                 	under normal conditions at 27°C. The most significant metabolic changes between
ST:STUDY_SUMMARY                 	these strains were related to amino acid metabolism, purine metabolism, and
ST:STUDY_SUMMARY                 	carboxylic acid metabolism.
ST:INSTITUTE                     	University of Puerto Rico, Medical Sciences Campus
ST:DEPARTMENT                    	Biochemistry
ST:LAST_NAME                     	Chorna
ST:FIRST_NAME                    	Nataliya
ST:ADDRESS                       	University of Puerto Rico, Medical Sciences Campus, Department of Biochemistry,
ST:ADDRESS                       	Main Building, 6th Floor, Room A-632, San Juan, PR 00935
ST:EMAIL                         	nataliya.chorna@upr.edu
ST:PHONE                         	7877582525 ext 1640
ST:NUM_GROUPS                    	2
ST:TOTAL_SUBJECTS                	14
#SUBJECT
SU:SUBJECT_TYPE                  	Yeast
SU:SUBJECT_SPECIES               	Saccharomyces cerevisiae
SU:TAXONOMY_ID                   	4932
SU:GENOTYPE_STRAIN               	BY4742, YGR023w
SU:CELL_BIOSOURCE_OR_SUPPLIER    	Open Biosystems
#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           	-	BY4742-1	Strain:Wild-type	RAW_FILE_NAME=BY4742-1.qgd; OD600=2.921
SUBJECT_SAMPLE_FACTORS           	-	BY4742-2	Strain:Wild-type	RAW_FILE_NAME=BY4742-2.qgd; OD600=3.562
SUBJECT_SAMPLE_FACTORS           	-	BY4742-3	Strain:Wild-type	RAW_FILE_NAME=BY4742-3.qgd; OD600=3.553
SUBJECT_SAMPLE_FACTORS           	-	BY4742-4	Strain:Wild-type	RAW_FILE_NAME=BY4742-4.qgd; OD600=2.514
SUBJECT_SAMPLE_FACTORS           	-	BY4742-5	Strain:Wild-type	RAW_FILE_NAME=BY4742-5.qgd; OD600=2.538
SUBJECT_SAMPLE_FACTORS           	-	BY4742-6	Strain:Wild-type	RAW_FILE_NAME=BY4742-6.qgd; OD600=3.102
SUBJECT_SAMPLE_FACTORS           	-	BY4742-7	Strain:Wild-type	RAW_FILE_NAME=BY4742-7.qgd; OD600=3.059
SUBJECT_SAMPLE_FACTORS           	-	YGR023w-1	Strain:mtl1Δ	RAW_FILE_NAME=YGR023w-1.qgd; OD600=3.296
SUBJECT_SAMPLE_FACTORS           	-	YGR023w-2	Strain:mtl1Δ	RAW_FILE_NAME=YGR023w-2.qgd; OD600=3.608
SUBJECT_SAMPLE_FACTORS           	-	YGR023w-3	Strain:mtl1Δ	RAW_FILE_NAME=YGR023w-3.qgd; OD600=3.466
SUBJECT_SAMPLE_FACTORS           	-	YGR023w-4	Strain:mtl1Δ	RAW_FILE_NAME=YGR023w-4.qgd; OD600=3.436
SUBJECT_SAMPLE_FACTORS           	-	YGR023w-5	Strain:mtl1Δ	RAW_FILE_NAME=YGR023w-5.qgd; OD600=3.322
SUBJECT_SAMPLE_FACTORS           	-	YGR023w-6	Strain:mtl1Δ	RAW_FILE_NAME=YGR023w-6.qgd; OD600=3.163
SUBJECT_SAMPLE_FACTORS           	-	YGR023w-7	Strain:mtl1Δ	RAW_FILE_NAME=YGR023w-7.qgd; OD600=3.208
#COLLECTION
CO:COLLECTION_SUMMARY            	Cells were grown at 27°C, 210 rpm in 5 mL of complete synthetic medium (CSM,
CO:COLLECTION_SUMMARY            	0.67% Nitrogen base without amino acids and ammonium sulfate, 2% glucose). The
CO:COLLECTION_SUMMARY            	next day, cells were replaced with fresh CSM and grow at 27°C to reach an OD of
CO:COLLECTION_SUMMARY            	0.6 - 0.7. 25 ml of each sample were harvested by centrifugation at 3,838 x g
CO:COLLECTION_SUMMARY            	for 5 min at 4°C, washed with 1 ml ice cold sterile water, quenched using ice
CO:COLLECTION_SUMMARY            	cold methanol, and stored at -80°C.
CO:SAMPLE_TYPE                   	Yeast cells
#TREATMENT
TR:TREATMENT_SUMMARY             	No treatment
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Extraction of metabolites was performed by homogenization in 1 mL of cold
SP:SAMPLEPREP_SUMMARY            	methanol/H2O (1:1) extraction solution and centrifugated at 167 x g at 4°C for
SP:SAMPLEPREP_SUMMARY            	5 min. Supernatants were collected and evaporated to dryness in a nitrogen
SP:SAMPLEPREP_SUMMARY            	stream stream at 50 ºC (RapidVap, Labconco), and derivatized by
SP:SAMPLEPREP_SUMMARY            	methoxyamination by adding 50 μl of 20 mg/ml solution of methoxyamine
SP:SAMPLEPREP_SUMMARY            	hydrochloride in pyridine followed by incubation at 37°C for 2 hours.
SP:SAMPLEPREP_SUMMARY            	Trimethylsilylation was subsequently performed by adding 50 µl of
SP:SAMPLEPREP_SUMMARY            	N-methyl-N-trimethylsilyl-trifluoroacetamide (MSTFA+1% TMCS) and incubated for 1
SP:SAMPLEPREP_SUMMARY            	hour at 65°C. Samples were centrifuged at 13000 rpm for 10 minutes at RT.
SP:SAMPLEPREP_SUMMARY            	Supernatants were transferred to glass vials for GC/MS analysis
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	GC
CH:INSTRUMENT_NAME               	Shimadzu GCMS-QP2010 ultra
CH:COLUMN_NAME                   	Shimadzu SH-Rxi-5ms (30 x 0.25 x 0.25)
CH:INTERNAL_STANDARD             	1 mM 2-Fluobiphenyl
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Shimadzu QP2010 Ultra
MS:INSTRUMENT_TYPE               	Single quadrupole
MS:MS_TYPE                       	EI
MS:ION_MODE                      	POSITIVE
MS:MS_COMMENTS                   	Inlet temperature was 280 °C; ion source temperature was 200 °C. MS
MS:MS_COMMENTS                   	conditions were set as follows: full scan mode, electron energy of 70 eV,
MS:MS_COMMENTS                   	quadrupole scan range of m/z 35–700. Data were processed using the GCMS
MS:MS_COMMENTS                   	Solution Postrun Analysis software (Shimadzu Inc) for metabolites identification
MS:MS_COMMENTS                   	from their electron impact mass spectra by comparison to the NIST 2014 spectral
MS:MS_COMMENTS                   	mass library.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	mM
MS_METABOLITE_DATA_START
Samples	BY4742-1	BY4742-2	BY4742-3	BY4742-4	BY4742-5	BY4742-6	BY4742-7	YGR023w-1	YGR023w-2	YGR023w-3	YGR023w-4	YGR023w-5	YGR023w-6	YGR023w-7
Factors	Strain:Wild-type	Strain:Wild-type	Strain:Wild-type	Strain:Wild-type	Strain:Wild-type	Strain:Wild-type	Strain:Wild-type	Strain:mtl1Δ	Strain:mtl1Δ	Strain:mtl1Δ	Strain:mtl1Δ	Strain:mtl1Δ	Strain:mtl1Δ	Strain:mtl1Δ
L-Lactic acid	0.014857352	0.028074116	0.003726308	0.085546368	0.068117045	0.025063755	0.040608841	0.003798906	0.010012303	0.008807549	0.00593959	0.00988884	0.020476803	0.020636584
Glycolic acid	0.001565768	0.000226141	0.000226714	0.002047955	0.001937546	0.015161001	0.003284716	0.001771703	0.001116289	0.009178771	0.003493894	0.001691042	0.001495817	0.002271027
L-Alanine	0.259471613	0.095671649	0.094344599	0.223810158	0.128060251	0.292930359	0.372061849	0.109360826	0.028063442	0.293722636	0.275056488	0.211757792	0.276065807	0.279554034
Glycine	0.191972956	0.069605109	0.074617042	0.195940152	0.194461432	0.205699548	0.243866673	0.053222136	0.030426871	0.165480984	0.094208208	0.155196474	0.179752728	0.213677101
L-Valine	0.208140003	0.093970068	0.092095536	0.192464317	0.103246167	0.243142963	0.267821773	0.091841688	0.047623161	0.211484607	0.145173571	0.188691423	0.250795647	0.253673909
L-Leucine	0.302401386	0.072921666	0.06528016	0.339152024	0.252311636	0.287274816	0.292831544	0.132889264	0.033722579	0.187575999	0.105888335	0.212520738	0.281522264	0.281252666
Niacinamide	0.057995723	0.010485747	0.013068062	0.11541365	0.056601707	0.052426448	0.067164646	0.009118635	0.008088301	0.046114248	0.034993318	0.043911391	0.059340055	0.055875761
L-Isoleucine	0.141372171	0.02216449	0.026381076	0.064157105	0.043086382	0.161360259	0.190105316	0.031514611	0.015763248	0.111588262	0.056482468	0.106638793	0.174654939	0.185695556
Pyrrolidonecarboxylic acid	0.121480524	0.157512208	0.189618858	0.256493779	0.133858388	0.088275879	0.190406667	0.100186331	0.241599878	0.241448895	0.316724227	0.232539699	0.256976906	0.254571991
Succinic acid	0.042892054	0.089479657	0.090192369	0.262497937	0.120576269	0.07279624	0.10671618	0.020356033	0.09084013	0.18354584	0.269258153	0.07054114	0.109625165	0.09616148
Uracil	0.082541276	0.02832587	0.032008083	0.188920274	0.119379606	0.115336405	0.119017298	0.019626352	0.056520143	0.089199569	0.105323536	0.077866889	0.11055295	0.097439891
L-Proline	0.055823284	0.026198851	0.025309355	0.185441286	0.068913077	0.074421296	0.093327932	0.0188448	0.002288858	0.054837644	0.021752414	0.035297751	0.05861539	0.061285612
Fumaric acid	0.006283039	0.004454486	0.005901385	0.019619613	0.014215962	0.014950371	0.009048264	0.010941438	0.00557885	0.014193314	0.021782172	0.012450996	0.012941504	0.009183174
L-Homoserine	0.013566386	0.002696827	0.004484419	0.009118759	0.007458831	0.013286015	0.004130009	0.002051073	0.01141914	0.026680342	0.03777816	0.02481049	0.016182844	0.015089866
Sarcosine	0.021634721	0.004045914	0.00340055	0.000805875	0.000798254	0.008183039	0.020933029	0.008262533	0.002807606	0.018113113	0.020291204	0.005497944	0.005390263	0.005864669
Pyroglutamic acid	0.308480201	0.438822919	0.45843804	0.408580383	0.433060255	0.282885405	0.247396811	0.444062305	0.367358768	0.311221795	0.46975196	0.240160142	0.247796544	0.202585494
L-Methionine	0.118315217	0.008438672	0.010850699	0.078311446	0.080498234	0.118476184	0.055081933	0.013414262	0.006075877	0.00126496	0.001276005	0.027071704	0.033101487	0.014852727
N-Acetylglutamic acid	0.306462228	0.350450074	0.377021717	0.579989658	0.57704236	0.252535746	0.171083407	0.379402711	0.295181167	0.301832129	0.521461968	0.292171223	0.336322625	0.137575942
L-Serine	0.245222792	0.312939646	0.309413572	0.24648616	0.154088133	0.228407652	0.142890479	0.306273033	0.229522476	0.141690336	0.182138018	0.204989199	0.190970225	0.180130624
L-Threonine	0.117936558	0.139168306	0.087405465	0.094661285	0.097138478	0.145310316	0.091467441	0.101718074	0.02610444	0.040448511	0.068087332	0.036739936	0.031493129	0.028604231
Ureidopropionic acid	0.083184426	0.098059243	0.195773444	0.159638008	0.149518549	0.098251006	0.067052255	0.067843899	0.097187869	0.187309383	0.184773233	0.144722207	0.135455149	0.014776744
Myristic acid	0.019289316	0.005217912	0.018798091	0.038459275	0.012480879	0.003136099	0.003084027	0.000511352	0.004869583	0.002431355	0.017825104	0.004955178	0.004176247	0.003943216
L-Phenylalanine	0.160303318	0.04033653	0.026277795	0.0261444	0.038452145	0.146403117	0.115752078	0.078390676	0.003118178	0.003245928	0.003274268	0.022545292	0.01778436	0.024424875
Malic acid	0.196936316	0.235579348	0.340875564	0.403450555	0.330615881	0.26190361	0.174166045	0.060365717	0.125757747	0.031623875	0.092121564	0.162646674	0.146554293	0.137575942
L-Aspartic acid	0.282154866	0.454006019	0.409719965	0.494678045	0.498170781	0.326595145	0.239111361	0.376108225	0.01746758	0.050298903	0.013290706	0.210684757	0.091608586	0.150348682
Malonic acid	0.044772626	0.033242223	0.094509004	0.091450507	0.044429168	0.001435893	0.017282979	0.016830127	0.012972614	0.036189402	0.028334325	0.026579465	0.018533774	0.006942239
L-Cysteine	0.066186123	0.046622716	0.092008689	0.017148945	0.076878544	0.075640696	0.091747777	0.018056879	0.008060249	0.09001335	0.017820967	0.052289052	0.001838848	0.001813053
Hypoxanthine	0.031183433	0.016049744	0.028363101	0.103713403	0.074172987	0.041972731	0.036360817	0.004637787	0.004643362	0.016050329	0.009942843	0.022672573	0.018776193	0.029686266
Palmitoleic acid	0.054189681	0.057239173	0.08078293	0.17528599	0.098433492	0.02571076	0.062060458	0.013848892	0.060267721	0.072762451	0.170855175	0.002656924	0.080493529	0.002845757
L-Glutamic acid	0.262311738	0.496963058	0.500969115	0.517521454	0.504756383	0.370977914	0.255431643	0.423561022	0.344757966	0.268986388	0.391192079	0.227599835	0.266971858	0.263861409
Ornithine	0.281099057	0.172587704	0.227886692	0.410938051	0.274561969	0.2212898	0.209932745	0.125755762	0.00130188	0.103861387	0.007849385	0.032532437	0.001485041	0.007321048
Palmitic acid	0.080525914	0.018943815	0.00785327	0.141187928	0.10608711	0.009309738	0.019837886	0.015585805	0.01672094	0.045063602	0.083446655	0.04315758	0.055275611	0.036368064
L-Asparagine	0.252737412	0.315085723	0.341086414	0.368257421	0.272197876	0.252605456	0.218661058	0.169693643	0.007765216	0.132684406	0.032200381	0.138101787	0.027000885	0.084393832
Homocysteine	0.019779664	0.014363173	0.012555553	0.032330303	0.01665115	0.022362383	0.021234757	0.002350114	0.008857057	0.021813774	0.005029129	0.00997354	0.010823211	0.020544543
Aminoadipic acid	0.273060252	0.571071985	0.516009784	0.552327643	0.226655407	0.290824829	0.253759632	0.350489234	0.163651766	0.211135937	0.033483785	0.215757919	0.196778004	0.199127539
Orotic acid	0.091558952	0.072327234	0.007693671	0.329465053	0.32161263	0.094295454	0.082337933	0.022723157	0.037962612	0.067141416	0.00159113	0.00159113	0.142360084	0.066367114
L-Glutamine	0.275182865	0.350421739	0.367424423	0.481331163	0.355738134	0.312749512	0.289250153	0.183740006	0.001516258	0.06098181	0.366357344	0.240961904	0.008647894	0.001705317
Oleic acid	0.021734892	0.029696209	0.027687031	0.056170352	0.01809352	0.01041561	0.024482455	0.008076193	0.026873328	0.034398598	0.05953699	0.001549426	0.001683157	0.021506418
Stearic acid	0.00908326	0.004772573	0.0087689	0.05072047	0.054927854	0.000706279	0.010584452	0.00644155	0.003743665	0.037255351	0.051668059	0.029699204	0.022501911	0.020945422
Eicosadienoic acid	0.026193285	0.006428955	0.01186227	0.034400032	0.012793024	0.000957033	0.025109706	0.002764515	0.006606629	0.027784346	0.049912369	0.018109124	0.032767862	0.034972219
L-Histidine	0.276222556	0.583718904	0.524773877	0.480550525	0.48555898	0.312094647	0.278870792	0.413284655	0.0576866	0.267308232	0.012114858	0.226467981	0.263631131	0.276468085
Citric acid	0.176484624	0.090021553	0.120190366	0.167400672	0.16936686	0.196060103	0.150535663	0.030511999	0.031770129	0.057642282	0.108546253	0.076737749	0.067916753	0.048136257
L-Tyrosine	0.231719021	0.459609819	0.470231326	0.111983659	0.135174387	0.246937842	0.264218171	0.245534215	0.107917748	0.231601543	0.091409076	0.192088903	0.248847949	0.2592758
L-Tryptophan	0.091205775	0.101745412	0.103779955	0.022580093	0.048945176	0.117306579	0.158094302	0.081665421	0.007762402	0.032630925	0.001630195	0.089425024	0.111749994	0.164348295
L-Cystathionine	0.244030985	0.027028138	0.013713277	0.007212059	0.305211715	0.064001359	0.055026666	0.091622377	0.000948547	0.026654863	0.084034476	0.094416524	0.101499608	0.139125595
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	quantified m/z	KEGG
L-Lactic acid	90	C00256
Glycolic acid	76	C03547
L-Alanine	89	C00041
Glycine	75	C00037
L-Valine	117	C00183
L-Leucine	131	C00123
Niacinamide	122	C00153
L-Isoleucine	131	C00407
Pyrrolidonecarboxylic acid	129	C02237
Succinic acid	118	C00042
Uracil	112	C00106
L-Proline	115	C00148
Fumaric acid	116	C00122
L-Homoserine	119	C00263
Sarcosine	89	C00213
Pyroglutamic acid	129	C01879
L-Methionine	149	C00073
N-Acetylglutamic acid	189	C00624
L-Serine	105	C00065
L-Threonine	119	C00188
Ureidopropionic acid	132	C02642
Myristic acid	228	C06424
L-Phenylalanine	165	C00079
Malic acid	134	C03668
L-Aspartic acid	133	C00049
Malonic acid	104	C04025
L-Cysteine	121	C00097
Hypoxanthine	136	C00262
Palmitoleic acid	254	C08362
L-Glutamic acid	147	C00025
Ornithine	132	C00077
Palmitic acid	256	C00249
L-Asparagine	132	C00152
Homocysteine	135	C05330
Aminoadipic acid	161	C00956
Orotic acid	156	C00295
L-Glutamine	146	C00064
Oleic acid	282	C00712
Stearic acid	284	C01530
Eicosadienoic acid	308	C16525
L-Histidine	155	C00135
Citric acid	192	C00158
L-Tyrosine	181	C00082
L-Tryptophan	204	C00078
L-Cystathionine	222	C02291
METABOLITES_END
#END