#METABOLOMICS WORKBENCH michaelsa93_20160428_121518 DATATRACK_ID:611 STUDY_ID:ST000395 ANALYSIS_ID:AN000632 PROJECT_ID:PR000308
VERSION             	1
CREATED_ON             	May 10, 2016, 12:37 pm
#PROJECT
PR:PROJECT_TITLE                 	The circadian oscillator in Synechococcus elongatus controls metabolite
PR:PROJECT_TITLE                 	partitioning during diurnal growth
PR:PROJECT_SUMMARY               	Cyanobacteria are increasingly being considered for use in large-scale outdoor
PR:PROJECT_SUMMARY               	production of fuels and industrial chemicals. Cyanobacteria can anticipate daily
PR:PROJECT_SUMMARY               	changes in light availability using an internal circadian clock and rapidly
PR:PROJECT_SUMMARY               	alter their metabolic processes in response to changes light availability.
PR:PROJECT_SUMMARY               	Understanding how signals from the internal circadian clock and external light
PR:PROJECT_SUMMARY               	availability are integrated to control metabolic shifts will be important for
PR:PROJECT_SUMMARY               	engineering cyanobacteria for production in natural outdoor environments. This
PR:PROJECT_SUMMARY               	study has assessed how “knowing” the correct time of day, via the circadian
PR:PROJECT_SUMMARY               	clock, affects metabolic changes when a cyanobacterium goes through a
PR:PROJECT_SUMMARY               	dark-to-light transition. Our data show that the circadian clock plays an
PR:PROJECT_SUMMARY               	important role in inhibiting activation of the oxidative pentose phosphate
PR:PROJECT_SUMMARY               	pathway in the morning. Synechococcus elongatus PCC 7942 is a genetically
PR:PROJECT_SUMMARY               	tractable model cyanobacterium that has been engineered to produce industrially
PR:PROJECT_SUMMARY               	relevant biomolecules and is the best-studied model for a prokaryotic circadian
PR:PROJECT_SUMMARY               	clock. However, the organism is commonly grown in continuous light in the
PR:PROJECT_SUMMARY               	laboratory, and data on metabolic processes under diurnal conditions are
PR:PROJECT_SUMMARY               	lacking. Moreover, the influence of the circadian clock on diurnal metabolism
PR:PROJECT_SUMMARY               	has been investigated only briefly. Here, we demonstrate that the circadian
PR:PROJECT_SUMMARY               	oscillator influences rhythms of metabolism during diurnal growth, even though
PR:PROJECT_SUMMARY               	light–dark cycles can drive metabolic rhythms independently. Moreover, the
PR:PROJECT_SUMMARY               	phenotype associated with loss of the core oscillator protein, KaiC, is distinct
PR:PROJECT_SUMMARY               	from that caused by absence of the circadian output transcriptional regulator,
PR:PROJECT_SUMMARY               	RpaA (regulator of phycobilisome-associated A). Although RpaA activity is
PR:PROJECT_SUMMARY               	important for carbon degradation at night, KaiC is dispensable for those
PR:PROJECT_SUMMARY               	processes. Untargeted metabolomics analysis and glycogen kinetics suggest that
PR:PROJECT_SUMMARY               	functional KaiC is important for metabolite partitioning in the morning.
PR:PROJECT_SUMMARY               	Additionally, output from the oscillator functions to inhibit RpaA activity in
PR:PROJECT_SUMMARY               	the morning, and kaiC-null strains expressing a mutant KaiC phosphomimetic,
PR:PROJECT_SUMMARY               	KaiC-pST, in which the oscillator is locked in the most active output state,
PR:PROJECT_SUMMARY               	phenocopies a ΔrpaA strain. Inhibition of RpaA by the oscillator in the morning
PR:PROJECT_SUMMARY               	suppresses metabolic processes that normally are active at night, and kaiC-null
PR:PROJECT_SUMMARY               	strains show indications of oxidative pentose phosphate pathway activation as
PR:PROJECT_SUMMARY               	well as increased abundance of primary metabolites. Inhibitory clock output may
PR:PROJECT_SUMMARY               	serve to allow secondary metabolite biosynthesis in the morning, and some
PR:PROJECT_SUMMARY               	metabolites resulting from these processes may feed back to reinforce clock
PR:PROJECT_SUMMARY               	timing.
PR:INSTITUTE                     	UC Davis
PR:DEPARTMENT                    	Genome and Biomedical Sciences Facility
PR:LABORATORY                    	WCMC Metabolomics Core
PR:LAST_NAME                     	Fiehn
PR:FIRST_NAME                    	Oliver
PR:ADDRESS                       	Health Sciences Drive, Davis, California, 95616, USA
PR:EMAIL                         	ofiehn@ucdavis.edu
PR:PHONE                         	(530) 754-8258
PR:FUNDING_SOURCE                	NIH U24DK097154
PR:PUBLICATIONS                  	doi: 10.1073/pnas.1504576112
#STUDY
ST:STUDY_TITLE                   	The circadian oscillator in Synechococcus elongatus controls metabolite
ST:STUDY_TITLE                   	partitioning during diurnal growth (part II)
ST:STUDY_SUMMARY                 	Cyanobacteria are increasingly being considered for use in large-scale outdoor
ST:STUDY_SUMMARY                 	production of fuels and industrial chemicals. Cyanobacteria can anticipate daily
ST:STUDY_SUMMARY                 	changes in light availability using an internal circadian clock and rapidly
ST:STUDY_SUMMARY                 	alter their metabolic processes in response to changes light availability.
ST:STUDY_SUMMARY                 	Understanding how signals from the internal circadian clock and external light
ST:STUDY_SUMMARY                 	availability are integrated to control metabolic shifts will be important for
ST:STUDY_SUMMARY                 	engineering cyanobacteria for production in natural outdoor environments. This
ST:STUDY_SUMMARY                 	study has assessed how “knowing” the correct time of day, via the circadian
ST:STUDY_SUMMARY                 	clock, affects metabolic changes when a cyanobacterium goes through a
ST:STUDY_SUMMARY                 	dark-to-light transition. Our data show that the circadian clock plays an
ST:STUDY_SUMMARY                 	important role in inhibiting activation of the oxidative pentose phosphate
ST:STUDY_SUMMARY                 	pathway in the morning. Synechococcus elongatus PCC 7942 is a genetically
ST:STUDY_SUMMARY                 	tractable model cyanobacterium that has been engineered to produce industrially
ST:STUDY_SUMMARY                 	relevant biomolecules and is the best-studied model for a prokaryotic circadian
ST:STUDY_SUMMARY                 	clock. However, the organism is commonly grown in continuous light in the
ST:STUDY_SUMMARY                 	laboratory, and data on metabolic processes under diurnal conditions are
ST:STUDY_SUMMARY                 	lacking. Moreover, the influence of the circadian clock on diurnal metabolism
ST:STUDY_SUMMARY                 	has been investigated only briefly. Here, we demonstrate that the circadian
ST:STUDY_SUMMARY                 	oscillator influences rhythms of metabolism during diurnal growth, even though
ST:STUDY_SUMMARY                 	light–dark cycles can drive metabolic rhythms independently. Moreover, the
ST:STUDY_SUMMARY                 	phenotype associated with loss of the core oscillator protein, KaiC, is distinct
ST:STUDY_SUMMARY                 	from that caused by absence of the circadian output transcriptional regulator,
ST:STUDY_SUMMARY                 	RpaA (regulator of phycobilisome-associated A). Although RpaA activity is
ST:STUDY_SUMMARY                 	important for carbon degradation at night, KaiC is dispensable for those
ST:STUDY_SUMMARY                 	processes. Untargeted metabolomics analysis and glycogen kinetics suggest that
ST:STUDY_SUMMARY                 	functional KaiC is important for metabolite partitioning in the morning.
ST:STUDY_SUMMARY                 	Additionally, output from the oscillator functions to inhibit RpaA activity in
ST:STUDY_SUMMARY                 	the morning, and kaiC-null strains expressing a mutant KaiC phosphomimetic,
ST:STUDY_SUMMARY                 	KaiC-pST, in which the oscillator is locked in the most active output state,
ST:STUDY_SUMMARY                 	phenocopies a ΔrpaA strain. Inhibition of RpaA by the oscillator in the morning
ST:STUDY_SUMMARY                 	suppresses metabolic processes that normally are active at night, and kaiC-null
ST:STUDY_SUMMARY                 	strains show indications of oxidative pentose phosphate pathway activation as
ST:STUDY_SUMMARY                 	well as increased abundance of primary metabolites. Inhibitory clock output may
ST:STUDY_SUMMARY                 	serve to allow secondary metabolite biosynthesis in the morning, and some
ST:STUDY_SUMMARY                 	metabolites resulting from these processes may feed back to reinforce clock
ST:STUDY_SUMMARY                 	timing.
ST:INSTITUTE                     	UC Davis
ST:DEPARTMENT                    	Genome and Biomedical Sciences Facility
ST:LABORATORY                    	WCMC Metabolomics Core
ST:LAST_NAME                     	Fiehn
ST:FIRST_NAME                    	Oliver
ST:ADDRESS                       	Health Sciences Drive, Davis, California, 95616, USA
ST:EMAIL                         	ofiehn@ucdavis.edu
ST:PHONE                         	(530) 754-8258
ST:STUDY_COMMENTS                	The first 4 samples were a test run to see how efficient the analysis was and
ST:STUDY_COMMENTS                	were run on a lipidomics platform. The next 12 samples were the used in the
ST:STUDY_COMMENTS                	paper and were the same as the original 4 samples, but they were split into 3
ST:STUDY_COMMENTS                	biological replicates and run on the GC platform.
ST:PUBLICATIONS                  	doi: 10.1073/pnas.1504576112
#SUBJECT
SU:SUBJECT_TYPE                  	Cells
SU:SUBJECT_SPECIES               	
Synechococcus elongatus PCC 7942
SU:TAXONOMY_ID                   	1140
#SUBJECT_SAMPLE_FACTORS:         	SUBJECT(optional)[tab]SAMPLE[tab]FACTORS(NAME:VALUE pairs separated by |)[tab]Additional sample data
SUBJECT_SAMPLE_FACTORS           	WT_C_T0_005	140619dlvsa11_1	Genotype:WT | Time Point:-	
SUBJECT_SAMPLE_FACTORS           	WT_B_T4_004	140619dlvsa12_2	Genotype:WT | Time Point:4	
SUBJECT_SAMPLE_FACTORS           	WT_B_T0_003	140619dlvsa03_1	Genotype:WT | Time Point:-	
SUBJECT_SAMPLE_FACTORS           	WT_C_T4_006	140619dlvsa02_1	Genotype:WT | Time Point:4	
SUBJECT_SAMPLE_FACTORS           	WT_A_T0_001	140619dlvsa05_1	Genotype:WT | Time Point:-	
SUBJECT_SAMPLE_FACTORS           	WT_A_T4_002	140619dlvsa04_1	Genotype:WT | Time Point:4	
SUBJECT_SAMPLE_FACTORS           	KaiC_B T0_009	140619dlvsa01_1	Genotype:KaiC mutant | Time Point:-	
SUBJECT_SAMPLE_FACTORS           	KaiC_C T0_011	140619dlvsa06_2	Genotype:KaiC mutant | Time Point:-	
SUBJECT_SAMPLE_FACTORS           	KaiC_A T0_007	140619dlvsa07_2	Genotype:KaiC mutant | Time Point:-	
SUBJECT_SAMPLE_FACTORS           	KaiC_A T4_008	140619dlvsa08_3	Genotype:KaiC mutant | Time Point:4	
SUBJECT_SAMPLE_FACTORS           	KaiC_B T4_010	140619dlvsa09_2	Genotype:KaiC mutant | Time Point:4	
SUBJECT_SAMPLE_FACTORS           	KaiC_C T4_012	140619dlvsa10_2	Genotype:KaiC mutant | Time Point:4	
#COLLECTION
CO:COLLECTION_SUMMARY            	Bacteria were grown in a turbidostat/bioreactor at equal cell density (measured
CO:COLLECTION_SUMMARY            	by optical density at 750nm), under a 12:12h Light/Dark cycle. After collection
CO:COLLECTION_SUMMARY            	samples were immediately placed on ice and then centrifuged at 5000RPM for 10min
CO:COLLECTION_SUMMARY            	at ­4 degrees Celsius. After centrifugation supernatant was decanted and cell
CO:COLLECTION_SUMMARY            	pellets were immediately frozen in liquid N2.
CO:COLLECTION_PROTOCOL_FILENAME  	StudyDesign-SpencerDiamond-10814.pdF
CO:COLLECTION_TIME               	Samples were collected at T0 (beginning of day) and T4 (4h into day).
CO:VOLUMEORAMOUNT_COLLECTED      	40ml of sample was collected at each time point
CO:STORAGE_CONDITIONS            	Samples were put into a 50mL conical tube containing ice up to the 30ml mark.
#TREATMENT
TR:TREATMENT_SUMMARY             	2: WT bacteria and KaiC mutant The phenotype associated with loss of the core
TR:TREATMENT_SUMMARY             	oscillator protein, KaiC, is distinct from that caused by absence of the
TR:TREATMENT_SUMMARY             	circadian output transcriptional regulator, RpaA (regulator of
TR:TREATMENT_SUMMARY             	phycobilisome-associated A). Untargeted metabolomics analysis and glycogen
TR:TREATMENT_SUMMARY             	kinetics suggest that functional KaiC is important for metabolite partitioning
TR:TREATMENT_SUMMARY             	in the morning. Additionally, output from the oscillator functions to inhibit
TR:TREATMENT_SUMMARY             	RpaA activity in the morning, and kaiC-null strains expressing a mutant KaiC
TR:TREATMENT_SUMMARY             	phosphomimetic, KaiC-pST, in which the oscillator is locked in the most active
TR:TREATMENT_SUMMARY             	output state, phenocopies a ΔrpaA strain. KaiC-null strains show indications of
TR:TREATMENT_SUMMARY             	oxidative pentose phosphate pathway activation as well as increased abundance of
TR:TREATMENT_SUMMARY             	primary metabolites. Inhibitory clock output may serve to allow secondary
TR:TREATMENT_SUMMARY             	metabolite biosynthesis in the morning, and some metabolites resulting from
TR:TREATMENT_SUMMARY             	these processes may feed back to reinforce clock timing.
TR:TREATMENT_PROTOCOL_FILENAME   	StudyDesign-SpencerDiamond-10814.pdf
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	1. Add 0.5mL of extraction solvent to tube, gently pipet to remove all cells,
SP:SAMPLEPREP_SUMMARY            	transfer cells to 2mL eppendorf tube. Repeat for a total of 1mL extraction
SP:SAMPLEPREP_SUMMARY            	solvent + cells in 2mL eppendorf tube. 2. Add 2 small stainless steel grinding
SP:SAMPLEPREP_SUMMARY            	beads to eppendorf tube 3. Use the GenoGrinder to grind for 3 minutes at 1,250
SP:SAMPLEPREP_SUMMARY            	rpm. 4. Centrifuge at 14,000xg for 5 minutes. 5. Transfer supernatant to a fresh
SP:SAMPLEPREP_SUMMARY            	2mL eppendorf tube. 6. Add 1mL of extraction solvent to tube containing cell
SP:SAMPLEPREP_SUMMARY            	pellet + beads, and repeat steps 3 and 4. 7. Collect supernatant, and combine
SP:SAMPLEPREP_SUMMARY            	with supernatant collected in step 5. Total volume of extracted sample will be
SP:SAMPLEPREP_SUMMARY            	approximately 2mL. 8. Dry down 50uL of extracted sample in 1.5mL eppendorf tube
SP:SAMPLEPREP_SUMMARY            	for GC-TOF analysis. 9. Store backups in -20 or -80C.
SP:SAMPLEPREP_PROTOCOL_FILENAME  	SOP_Extraction_of_Yeast_Cells.pdf
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_TYPE           	GC
CH:INSTRUMENT_NAME               	Leco Pegasus III GC
CH:COLUMN_NAME                   	Restek Rtx-5Sil MS (30 x 0.25mm, 0.25um)
CH:COLUMN_NAME                   	0.25 μm film made of 95% dimethyl/5%diphenylpolysiloxane)
CH:FLOW_RATE                     	1 ml/min
CH:COLUMN_TEMPERATURE            	50-330C
CH:METHODS_FILENAME              	SOP_Extraction_of_Yeast_Cells.pdf
CH:COLUMN_PRESSURE               	7.7 PSI
CH:INJECTION_TEMPERATURE         	50 C ramped to 250 C by 12 C/s
CH:SAMPLE_INJECTION              	0.5 uL
CH:OVEN_TEMPERATURE              	50°C for 1 min, then ramped at 20°C/min to 330°C, held constant for 5 min
CH:TRANSFERLINE_TEMPERATURE      	230C
CH:WASHING_BUFFER                	Ethyl Acetate
CH:SAMPLE_LOOP_SIZE              	30 m length x 0.25 mm internal diameter
CH:RANDOMIZATION_ORDER           	Excel generated
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
AN:LABORATORY_NAME               	WCMC Metabolomics Core
AN:DETECTOR_TYPE                 	TOF
AN:SOFTWARE_VERSION              	ChromaTOF
AN:DATA_FORMAT                   	.peg, .txt, .cdf
#MS
MS:MS_COMMENTS                   	-
MS:INSTRUMENT_NAME               	Leco Pegasus III GC TOF
MS:INSTRUMENT_TYPE               	GC-TOF
MS:MS_TYPE                       	EI
MS:ION_MODE                      	POSITIVE
MS:ION_SOURCE_TEMPERATURE        	250 C
MS:IONIZATION_ENERGY             	70 eV
MS:SOURCE_TEMPERATURE            	250 C
MS:SCAN_RANGE_MOVERZ             	85-500 Da
MS:SCANNING_CYCLE                	17 Hz
MS:SCANNING_RANGE                	85-500 Da
MS:SKIMMER_VOLTAGE               	1850 V
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS         	counts
MS_METABOLITE_DATA_START
	140619dlvsa11_1	140619dlvsa12_2	140619dlvsa03_1	140619dlvsa02_1	140619dlvsa05_1	140619dlvsa04_1	140619dlvsa01_1	140619dlvsa06_2	140619dlvsa07_2	140619dlvsa08_3	140619dlvsa09_2	140619dlvsa10_2
xylulose NIST	600	529	610	255	436	557	248	576	789	506	518	304
xanthosine	728	983	1090	992	723	1061	2208	1007	2048	1700	1135	1227
valine	2702	10267	4963	12700	4824	8305	9451	4708	7627	11747	17091	18313
uridine	14445	2383	14979	8100	8397	9238	18688	8382	8759	12112	7864	6355
urea	831	8730	6135	18187	7405	5890	2612	1147	3953	3108	5590	4213
uracil	3286	3239	2787	1895	3477	1943	2419	2591	2075	3743	2158	2293
UDP-N-acetylglucosamine	183	273	357	244	292	271	209	149	214	574	392	260
tyrosine	5302	7129	3337	9678	3702	7642	7982	6601	4697	10808	11169	11778
tryptophan	5004	4224	1880	5589	1982	6936	17133	26374	13675	18752	20812	35579
trans-4-hydroxy-L-proline	1087	1794	3100	1515	1936	1311	1182	1222	993	1328	927	563
thymine	6932	6863	6637	7893	6342	5279	10041	6598	6224	8504	4977	5226
thymidine-5-phosphate	2033	690	1121	435	711	427	2175	1496	653	1863	870	510
thymidine	7077	3279	4823	5598	4149	3864	5080	3771	3658	4830	2745	2400
threonine	1947	3489	2039	4239	2378	2956	4049	3035	2673	5111	5050	4875
threitol	1530	2659	2276	2425	2878	2213	1392	1083	1703	1995	1622	1375
sulfuric acid	10797	206	3833	167	921	1289	4268	8479	405	6753	325	279
sucrose	560	6345	448	6104	482	8370	2578	1323	2274	52732	46288	34140
stearic acid	269226	272593	206216	137203	287227	221562	171345	234654	225601	128578	148689	161548
spermidine	361	323	339	448	307	644	350	635	1541	709	1282	431
sorbitol	837	997	1147	515	619	363	777	532	666	763	1249	1569
serine	1899	4959	2732	11261	2233	3267	18106	2650	3578	6696	6211	5869
salicylaldehyde	1878	3241	2536	2396	1312	1755	1601	2899	2207	2177	3116	3289
ribose-5-phosphate	1454	1675	927	1660	1096	1769	876	1102	1343	1999	2212	1586
ribose	1527	3151	183	3212	1675	2919	2051	2280	2391	2577	1552	2957
ribonic acid	302	267	456	266	523	371	308	211	432	349	338	192
pyrophosphate	5172	5810	5154	3060	6758	11852	3980	2383	2219	14410	6445	3906
putrescine	1175	1003	1669	1955	3304	1104	828	736	2492	1101	2425	1456
propane-1,3-diol NIST	921	1648	2002	1568	1249	2045	1045	754	1562	1060	942	820
proline	357	768	1249	1348	2002	1094	1235	644	589	508	940	645
pimelic acid	1011	916	1064	1477	1799	1471	544	1174	982	912	708	860
phytol	59536	38022	73314	48760	59282	37398	73959	61141	64258	55688	42874	41752
phosphate	20719	56096	22398	52082	40430	27431	46372	70315	77209	28668	30762	22037
phenylalanine	657	706	593	1104	1221	764	798	181	627	217	804	757
pentadecanoic acid	2526	4094	3174	1917	3685	636	4317	3438	2667	4971	4617	4379
pelargonic acid	11584	13503	17783	10600	19162	13311	11141	8774	11703	14504	11106	10300
p-cresol	121793	117460	179180	103911	154086	117275	115565	76650	93378	104627	80404	65090
parabanic acid NIST	606	2504	4158	2027	3581	2585	2449	992	2623	2107	2513	3967
palmitoleic acid	162613	109167	212559	111336	165247	115270	134638	147522	115478	83128	95164	108998
palmitic acid	69867	69685	88856	50660	81753	62737	54306	55043	50285	43365	47490	50949
oxoproline	30097	224799	154997	332432	163547	180197	228608	91560	182136	249007	430621	454503
oxalic acid	285	320	499	326	1015	510	866	1181	125	1023	734	444
ornithine	632	1270	816	2562	1020	796	1223	1242	884	1363	791	569
oleic acid	9704	20202	28239	8995	8877	15184	20362	23994	20160	18891	24639	17277
oleamide NIST	854	1496	1457	464	2078	613	2665	1358	509	1976	1004	876
octanol NIST	655	824	1027	778	1203	818	1055	585	784	430	495	499
octadecanol	1255	643	1067	631	442	468	832	709	562	666	917	664
nicotinic acid	1122	829	727	948	718	773	771	471	418	697	853	507
nicotinamide	3495	4901	4840	5552	7412	4160	3172	2606	3804	2312	3438	3257
N-acetylglutamate	5883	5189	2818	6532	4979	1875	8512	6762	2717	15681	1630	1414
N-acetyl-D-mannosamine	319	269	334	360	254	282	230	179	334	556	394	303
myristic acid	17265	16175	21092	13423	21443	14713	18025	18356	14456	13430	14555	15027
methionine	548	499	653	1014	711	590	860	159	836	414	1328	1088
mannose-6-phosphate NIST	218	85	325	143	327	481	85	163	139	258	72	199
maltotriose	8583	3651	7638	3617	2611	3219	5444	8037	6416	3987	4517	6450
maltotriitol	392	428	394	334	343	145	536	285	393	226	306	215
maltose	1928	1633	2809	1201	2071	2066	1992	1138	1860	1421	1540	1831
maltitol	371	423	197	343	551	381	542	576	777	578	314	420
maleimide	1989	5579	9560	12183	8377	6611	12549	3696	5095	2319	3250	3858
lyxitol	287	560	625	671	556	522	461	193	386	808	499	449
lysopalmitoyl monogalactosylglycerol	172130	67682	140348	51913	49543	59804	71945	95024	69761	38142	43850	57936
lysine	3101	1089	1460	2550	3728	893	11105	14012	13102	2228	1548	2243
levoglucosan	390	706	562	981	980	779	812	404	673	951	744	653
leucine	894	4253	1934	5628	2071	2517	3309	1208	2676	2370	5516	5858
lauric acid	5707	7384	8491	6183	6913	6704	6093	6433	5470	6080	7339	7291
lactic acid	4356	9183	7068	22937	5545	8312	5156	2943	3674	3331	4947	3713
isothreonic acid	382	441	1084	657	980	895	528	594	452	590	595	690
isoleucine	468	2627	1897	4123	1840	1881	2274	764	1937	2107	4733	5006
inulotriose	245	296	422	411	513	408	965	1090	1376	1123	1043	979
hydroxylamine	24462	27246	39602	24253	34690	27141	25049	17648	22509	22727	17874	14798
homoserine	229	443	508	574	543	920	518	172	578	236	598	645
hexose-6-phosphate	311	607	277	607	409	638	359	320	446	726	579	862
heptadecanoic acid	3972	7165	3990	3269	5385	4732	4498	4389	4472	4328	4447	4910
guanosine	4631	7622	4304	4886	4926	5946	12780	11398	10644	11733	9812	7871
guanine	801	869	1041	868	1172	793	679	873	1376	662	667	905
glycolic acid	3153	3458	6195	3595	5464	3495	3094	2750	2690	2743	2624	2991
glycine	168	956	627	2087	736	719	1793	231	414	738	979	929
glycerol-alpha-phosphate	74147	41016	84178	45579	65878	53711	74442	64780	50526	55358	29973	44197
glycerol-3-galactoside	173238	72576	119191	90669	59871	67625	72265	120430	59618	33289	40307	70391
glycerol	49916	26839	20302	79922	106729	77020	16904	54056	85860	87034	17521	59295
glyceric acid	1418	1794	2245	1930	1941	2190	1797	1680	1518	2007	1695	2024
glutaric acid	344	361	593	459	188	416	260	318	212	355	216	344
glutamine	415	1362	804	934	1591	1175	1442	2258	2064	3270	2938	3108
glutamic acid	5864	5660	10707	5947	14825	15722	6385	5224	6254	23258	12228	10720
glucose-6-phosphate	833	1987	913	1372	637	1610	1096	1167	1130	5320	4290	4089
glucose-1-phosphate	2681	5725	3779	4200	2444	8548	5831	5184	4237	10681	6885	3394
glucose	63663	156855	99320	120410	71742	152854	145613	121555	131305	198026	217635	151712
gluconic acid	384	1001	662	714	835	2066	487	957	184	545	834	714
galactinol	279244	208492	129385	253529	148816	298446	129330	163934	117937	125726	134059	132784
fumaric acid	699	1010	1192	367	480	307	296	459	395	586	549	538
fucose	2434	2988	2667	3061	3687	4603	3501	2383	2942	3501	4105	2655
fructose-6-phosphate	443	1019	388	774	675	748	878	456	503	2751	2027	2036
fructose	1945	3223	3212	3034	1345	5011	5237	3808	2714	3387	3654	3965
erythrose	336	482	556	440	391	938	417	473	662	666	798	414
erythronic acid	436	1543	582	853	855	1264	900	822	1135	1162	938	691
enolpyruvate NIST	329	847	585	380	941	375	413	251	304	570	412	392
cytosin	191	806	545	1005	1084	891	284	218	644	385	644	737
cytidine	772	697	559	495	713	795	1710	1756	2198	1659	1557	990
citric acid	3965	18787	6064	8432	50809	16851	5749	5551	12676	14104	5598	3655
capric acid	1536	2683	2661	2201	3644	1943	1716	1514	1587	2175	1712	1980
butyrolactam NIST	531	1391	1295	1016	934	686	1132	578	698	597	494	701
beta-glycerolphosphate	726	1261	1209	679	1472	997	963	892	575	496	417	849
beta-alanine	250	927	194	253	457	273	173	193	359	275	229	565
benzoic acid	17706	17741	23499	16303	24095	20354	14335	12444	14347	15105	12995	11713
behenic acid	8632	21674	7259	18952	16244	22876	38877	19151	26415	42307	33262	27771
azelaic acid	1015	1281	670	1051	1289	1525	1315	1459	289	2046	656	1429
aspartic acid	1055	4356	4290	3481	5837	2070	5523	3365	4574	2565	4333	5081
asparagine	338	213	431	262	355	85	211	152	95	203	255	204
arachidic acid	37590	3543	4809	3241	3905	6656	7171	70912	84134	9199	6134	5833
alpha-ketoglutarate	950	2302	1489	2588	1200	1241	987	485	707	1736	1355	1557
alanine-alanine	248	475	382	253	398	274	191	145	362	252	258	421
alanine	8548	11958	11768	17066	10382	10680	24151	12244	13738	27389	21028	21827
adipic acid	2125	3189	3753	3316	3690	2894	2171	1666	2367	2739	1942	1837
adenosine	111755	106015	36060	95007	81017	111389	189643	200223	213457	212043	164373	137716
adenine	12060	24250	20393	25507	27785	19963	14974	14605	19351	16462	16172	14691
acetophenone NIST	3760	2981	4589	3322	6367	3760	4862	2306	1910	2222	2147	1681
6-deoxyglucose	4337	5322	5028	6112	6613	5391	3640	4994	3731	5656	5222	4284
5-hydroxymethyl-2-furoic acid NIST	359	17156	16882	240	525	309	161	240	257	566	214	299
5'-deoxy-5'-methylthioadenosine	218	461	299	350	393	253	2004	1657	1785	1868	899	501
4-hydroxybenzoate	638	938	710	1058	1583	651	363	533	852	445	652	283
3-phosphoglycerate	2333	3283	4318	3056	11633	6429	3718	4312	4153	9115	2984	2052
3-hydroxypropionic acid	908	974	690	1044	708	986	532	645	698	797	361	603
3-hydroxypalmitic acid	678	585	1124	446	421	495	1916	1905	1800	1374	1421	1504
2-ketoadipic acid	1582	1787	2687	1864	2187	1757	1182	1021	1525	1302	1148	1092
2-deoxytetronic acid	172	383	297	321	188	553	421	319	443	488	288	321
2'-deoxyguanosine	1064	741	368	462	678	590	743	4546	634	679	6785	589
2,3-dihydroxypyridine	394	614	482	422	272	597	828	486	543	324	463	349
1-monopalmitin	871	860	779	585	500	597	636	435	470	572	317	528
1-hexadecanol	602	446	847	627	574	448	383	342	596	478	304	325
1,2,4-benzenetriol	254	1019	3557	1095	3636	2459	520	462	530	340	647	596
2,5-dihydroxypyrazine NIST	724	647	727	499	990	1494	1271	1297	711	2409	494	794
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	retention index	quantified mz	KEGG ID	PubChem ID
xylulose NIST	553450	173	C00312	439205
xanthosine	926133	325	C01762	64959
valine	313502	144	C00183	6287
uridine	861508	217	C00299	6029
urea	326574	189	C00086	1176
uracil	385816	241	C00106	1174
UDP-N-acetylglucosamine	623789	226	C00043	445675
tyrosine	671252	218	C00082	6057
tryptophan	780482	202	C00078	6305
trans-4-hydroxy-L-proline	457910	158	C01157	5810
thymine	420133	255	C00178	1135
thymidine-5-phosphate	608111	170	C00364	9700
thymidine	349402	170	C00214	5789
threonine	409568	218	C00188	6288
threitol	467595	217	C16884	169019
sulfuric acid	282411	227	C00059	1118
sucrose	915139	271	C00089	5988
stearic acid	787622	117	C01530	5281
spermidine	792924	144	C00315	1102
sorbitol	667922	217	C00794	5780
serine	395020	218	C00065	5951
salicylaldehyde	406586	119	C06202	6998
ribose-5-phosphate	731096	315	C00117	439167
ribose	553135	217	C00121	5779
ribonic acid	599680	292	C01685	5460677
pyrophosphate	326948	110	C00013	1023
putrescine	588119	174	C00138	1049
propane-1,3-diol NIST	214380	177	C02457	10442
proline	364716	142	C00148	145742
pimelic acid	523205	155	C02656	385
phytol	761712	143	C01389	5280435
phosphate	345365	314	C00009	1004
phenylalanine	537804	218	C00079	6140
pentadecanoic acid	674647	117	C16537	13849
pelargonic acid	399229	117	C01601	8158
p-cresol	280360	165	C01468	2879
parabanic acid NIST	464991	100	C00802	67126
palmitoleic acid	706508	117	C08362	445638
palmitic acid	713809	313	C00249	985
oxoproline	485935	156	C01879	7405
oxalic acid	260513	190	C00209	971
ornithine	619548	142	C00077	6262
oleic acid	779120	339	C00712	445639
oleamide NIST	849710	144	C19670	5283387
octanol NIST	247010	187
octadecanol	755409	327		8221
nicotinic acid	366992	180	C00253	938
nicotinamide	471602	179	C00153	936
N-acetylglutamate	604748	216	C00624	70914
N-acetyl-D-mannosamine	726375	319
myristic acid	634414	117	C06424	11005
methionine	483560	176	C00073	6137
mannose-6-phosphate NIST	822643	387	C00275	65127
maltotriose	1179224	361	C01835	439586
maltotriitol	1214242	361		3625615
maltose	946601	204	C00208	439186
maltitol	976828	361	D04845	493591
maleimide	245118	154	C07272	10935
lyxitol	573587	217	C00532	439255
lysopalmitoyl monogalactosylglycerol	1183271	204		53483072
lysine	663483	156	C00047	5962
levoglucosan	569637	204		2724705
leucine	346101	158	C00123	6106
lauric acid	547906	117	C02679	3893
lactic acid	217657	191	C01432	612
isothreonic acid	489385	292	C00639	151152
isoleucine	359251	158	C00407	6306
inulotriose	1131821	361	C01355	22833608
hydroxylamine	255241	146	C00192	787
homoserine	443878	218	C00263	12647
hexose-6-phosphate	806282	387	C02965	208
heptadecanoic acid	751309	117		10465
guanosine	954962	324	C00387	6802
guanine	744307	352	C00242	764
glycolic acid	227636	177	C00160	757
glycine	368707	248	C00037	750
glycerol-alpha-phosphate	590747	357	C03189	754
glycerol-3-galactoside	805227	204	C05401	16048618
glycerol	344466	205	C00116	753
glyceric acid	377495	189	C00258	439194
glutaric acid	421596	261	C00489	743
glutamine	600315	156	C00064	5961
glutamic acid	529100	246	C00025	33032
glucose-6-phosphate	810287	387	C01172	439427
glucose-1-phosphate	594647	217	C00103	65533
glucose	650867	319	C00221	64689
gluconic acid	693148	333	C00800	6857417
galactinol	1048207	204	C01235	11727586
fumaric acid	390775	245	C00122	444972
fucose	578299	160	C02095	439650
fructose-6-phosphate	804279	315	C05345	440641
fructose	639442	307	C02336	439709
erythrose	443306	205	C01796	439574
erythronic acid	512029	217		2781043
enolpyruvate NIST	234394	217	C00074	1005
cytosin	486724	254	C00380	597
cytidine	937026	223	C00475	6175
citric acid	617342	273	C00158	311
capric acid	452386	229	C01571	2969
butyrolactam NIST	277199	142		12025
beta-glycerolphosphate	574470	243	C02979	2526
beta-alanine	435564	248	C00099	239
benzoic acid	339214	179	C00180	243
behenic acid	920648	117	C08281	8215
azelaic acid	610651	317	C08261	2266
aspartic acid	480387	232	C00049	5960
asparagine	553078	188	C00152	6267
arachidic acid	856421	117	C06425	10467
alpha-ketoglutarate	507392	198	C00026	51
alanine-alanine	636898	188	C00993	5484352
alanine	243971	116	C00041	5950
adipic acid	474435	111	C06104	196
adenosine	918039	236	C00212	60961
adenine	646534	264	C00147	190
acetophenone NIST	238615	105	C07113	7410
6-deoxyglucose	573663	117	C08352	441480
5-hydroxymethyl-2-furoic acid NIST	497561	123	C20448	80642
5'-deoxy-5'-methylthioadenosine	967036	236	C00170	439176
4-hydroxybenzoate	537925	223	C00156	135
3-phosphoglycerate	610734	227	C00597	724
3-hydroxypropionic acid	269265	177	C01013	68152
3-hydroxypalmitic acid	774930	233		15569776
2-ketoadipic acid	331841	100
2-deoxytetronic acid	433456	189		150929
2'-deoxyguanosine	962182	295	C00330	187790
2,3-dihydroxypyridine	373895	240		28115
1-monopalmitin	901749	129	C01885	14900
1-hexadecanol	679596	299	C00823	2682
1,2,4-benzenetriol	521803	239	C02814	10787
2,5-dihydroxypyrazine NIST	397526	241		23368901
METABOLITES_END
#END