#METABOLOMICS WORKBENCH cclish_20250406_182430 DATATRACK_ID:5820 STUDY_ID:ST003867 ANALYSIS_ID:AN006356 PROJECT_ID:PR002423
VERSION             	1
CREATED_ON             	April 9, 2025, 8:53 pm
#PROJECT
PR:PROJECT_TITLE                 	Fatty-acid oxidation is a metabolic hallmark of human proliferative retinopathy
PR:PROJECT_SUMMARY               	In this experiment, we used nontargeted metabolomics to measure metabolite
PR:PROJECT_SUMMARY               	profiles of vitreous humor from subjects with proliferative diabetic
PR:PROJECT_SUMMARY               	retinopathy. Vitreous samples were collected adjacent to leaky pathological
PR:PROJECT_SUMMARY               	neovascular tufts that characterize PR. Amongst the top 25 most significantly
PR:PROJECT_SUMMARY               	dysregulated metabolites, we observed an accumulation of acylcarnitines in human
PR:PROJECT_SUMMARY               	neovascular PR samples compared to control subjects with epiretinal membranes.
PR:INSTITUTE                     	Broad Institute of MIT and Harvard
PR:DEPARTMENT                    	Metabolomics Platform
PR:LAST_NAME                     	Clish
PR:FIRST_NAME                    	Clary
PR:ADDRESS                       	300 BineyStreet, Cambridge, MA, 02142, USA
PR:EMAIL                         	clary@broadinstitute.org
PR:PHONE                         	617-714-7654
PR:PUBLICATIONS                  	submitted
PR:CONTRIBUTORS                  	Gael Cagnone, Sheetal Pundir, Charlotte Betus, Tapan Agnihotri, Anli Ren, Jin
PR:CONTRIBUTORS                  	SungKim, Noémie-Rose Harvey, Emilie Heckel, Mei Xi Chen, Anu Situ, Perrine
PR:CONTRIBUTORS                  	Gaub, Nicholas Kim, Ashim Das, Severine Leclerc, Florian Wünnemann, Louis
PR:CONTRIBUTORS                  	Berillon, Gregor Andelfinger, Sergio Crespo-Garcia, Alexandre Dubrac, Flavio A.
PR:CONTRIBUTORS                  	Rezende, Clary B. Clish, Bruno Maranda, José Carlos Rivera, Lois E. H. Smith,
PR:CONTRIBUTORS                  	Przemyslaw Sapieha, JeanSébastien Joyal
#STUDY
ST:STUDY_TITLE                   	Fatty-acid oxidation is a metabolic hallmark of human proliferative retinopathy
ST:STUDY_TYPE                    	comparison of vitreous humor from subjects with proliferative diabetic
ST:STUDY_TYPE                    	retinopathy to epiretinal membrane (control)
ST:STUDY_SUMMARY                 	Healthy blood vessels supply neurons to preserve metabolic function. In blinding
ST:STUDY_SUMMARY                 	proliferative retinopathies (PRs), pathological neovascular tufts often emerge
ST:STUDY_SUMMARY                 	in lieu of needed physiological revascularization. Here we show that metabolic
ST:STUDY_SUMMARY                 	shifts in the neovascular niche define angiogenic fate. Fatty acid oxidation
ST:STUDY_SUMMARY                 	(FAO) metabolites accumulated in human and murine retinopathy samples.
ST:STUDY_SUMMARY                 	Neovascular tufts with a distinct single-cell transcriptional signature highly
ST:STUDY_SUMMARY                 	expressed FAO enzymes. The deletion of Sirt3, an FAO regulator, shifted the
ST:STUDY_SUMMARY                 	neovascular niche metabolism from FAO to glycolysis and suppressed tuft
ST:STUDY_SUMMARY                 	formation. This metabolic transition increased Vegf expression in astrocytes and
ST:STUDY_SUMMARY                 	reprogrammed pathological neovessels to a physiological phenotype, hastening
ST:STUDY_SUMMARY                 	vascular regeneration of the ischemic retina and improving vision. Hence,
ST:STUDY_SUMMARY                 	strategies to change the metabolic environment of vessels could promote a
ST:STUDY_SUMMARY                 	regenerative phenotype in vascular diseases. In this experiment, we used
ST:STUDY_SUMMARY                 	nontargeted metabolomics to measure metabolite profiles of vitreous humor from
ST:STUDY_SUMMARY                 	subjects with proliferative diabetic retinopathy. Vitreous samples were
ST:STUDY_SUMMARY                 	collected adjacent to leaky pathological neovascular tufts that characterize PR.
ST:STUDY_SUMMARY                 	Amongst the top 25 most significantly dysregulated metabolites, we observed an
ST:STUDY_SUMMARY                 	accumulation of acylcarnitines in human neovascular PR samples compared to
ST:STUDY_SUMMARY                 	control subjects with epiretinal membranes. Fatty acylcarnitines are by-products
ST:STUDY_SUMMARY                 	of fatty-acid beta-oxidation (FAO), the process of oxidizing fatty acids in
ST:STUDY_SUMMARY                 	mitochondria to produce acetyl-CoA (Fig. 1b). 5 of the 6 most enriched metabolic
ST:STUDY_SUMMARY                 	pathways in human PR pertained to FA metabolism, including long and short-chain
ST:STUDY_SUMMARY                 	saturated FAO pathways.
ST:INSTITUTE                     	Broad Institute of MIT and Harvard
ST:DEPARTMENT                    	Metabolomics Platform
ST:LAST_NAME                     	Clish
ST:FIRST_NAME                    	Clary
ST:ADDRESS                       	300 Binney Street, Cambridge, MA, 02142, USA
ST:EMAIL                         	clary@broadinstitute.org
ST:PHONE                         	617-714-7654
ST:NUM_GROUPS                    	2
ST:TOTAL_SUBJECTS                	15
ST:NUM_MALES                     	9
ST:NUM_FEMALES                   	6
#SUBJECT
SU:SUBJECT_TYPE                  	Human
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
SU:AGE_OR_AGE_RANGE              	35-84
SU:GENDER                        	Male and female
#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           	-	14	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sex=F; Age=46; Eye Collected=OS; Past Medical History=-; Medications=none; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0006_JOY_VitHum_HIL-ERM-14.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0006_JOY_ERM_CMH-14.raw
SUBJECT_SAMPLE_FACTORS           	-	15	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sex=F; Age=84; Eye Collected=OD; Past Medical History=Hypertension, Dyslipidemia; Medications=Warfarin, Fluoxetine; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0007_JOY_VitHum_HIL-ERM-15.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0007_JOY_ERM_CMH-15.raw
SUBJECT_SAMPLE_FACTORS           	-	16	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sex=M; Age=78; Eye Collected=OS; Past Medical History=Hypertension, Dyslipidemia, Coronary artery disease, Gout, Diabetes Type 2, Atrial fibrillation; Medications=Warfarin; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0008_JOY_VitHum_HIL-ERM-16.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0008_JOY_ERM_CMH-16.raw
SUBJECT_SAMPLE_FACTORS           	-	108	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sex=M; Age=57; Eye Collected=OS; Past Medical History=Hypertension; Medications=NifedipineIrbezartan/Hydrochlorothiazide, Acetaminophen; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0009_JOY_VitHum_HIL-ERM-108.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0009_JOY_ERM_CMH-108.raw
SUBJECT_SAMPLE_FACTORS           	-	136	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sex=M; Age=68; Eye Collected=OD; Past Medical History=Diabetes Type 1; Medications=Formoterol/ budesonide, Rosuvastatin, Calcium/Vit D, Perindopril/Erbumine, Tamsulosine; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=excluded; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0010_JOY_VitHum_HIL-ERM-136.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0010_JOY_ERM_CMH-136.raw
SUBJECT_SAMPLE_FACTORS           	-	85	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage and tractional retinal detachments	Sex=M; Age=74; Eye Collected=OD; Past Medical History=Diabetes Type 2, Dyslipidemia, Hypertension, stroke, Coronary artery disease; Medications=Warfarin, Metformin, Glicazide, Acetaminophen, Gabapentin, Biocal-D forte, Alendronate, Atorvastatin, AAS, Furosemide; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0031_JOY_VitHum_HIL-DR-85.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0031_JOY_DR_CMH-85.raw
SUBJECT_SAMPLE_FACTORS           	-	126	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with neovascular glaucoma	Sex=F; Age=79; Eye Collected=OS; Past Medical History=Diabetes Type 2, Hemodialysis, Hypertension, Coronary artery disease; Medications=NA; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=excluded; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0032_JOY_VitHum_HIL-DR-126.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0032_JOY_DR_CMH-126.raw
SUBJECT_SAMPLE_FACTORS           	-	124	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage and tractional retinal detachments	Sex=M; Age=35; Eye Collected=OD; Past Medical History=Diabetes Type 2; Medications=NA; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0033_JOY_VitHum_HIL-DR-124.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0033_JOY_DR_CMH-124.raw
SUBJECT_SAMPLE_FACTORS           	-	86	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage	Sex=F; Age=78; Eye Collected=OD; Past Medical History=Diabetes Type 2, Dyslipidemia, Hypertension, Renal insufficiency; Medications=Metformin, Formoterol/budesonide, Escitalopram, Vit D; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0034_JOY_VitHum_HIL-DR-86.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0034_JOY_DR_CMH-86.raw
SUBJECT_SAMPLE_FACTORS           	-	142	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with tractional retinal detachments	Sex=M; Age=36; Eye Collected=OD; Past Medical History=Diabetes Type 2, Stroke, Renal insufficiency; Medications=NA; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0035_JOY_VitHum_HIL-DR-142.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0035_JOY_DR_CMH-142.raw
SUBJECT_SAMPLE_FACTORS           	-	153	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with macular edema and pre-retinal hemorrhage	Sex=M; Age=45; Eye Collected=OD; Past Medical History=Diabetes Type 2, Dyslipidemia, Hypertension; Medications=Insulin, Diltiazem, EzetimibeRosuvastatin, Perindopril/Erbumine/IndapamideMontelukast, EmpagliflozineSemaglutide, AAS, Metformin; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=excluded; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0036_JOY_VitHum_HIL-DR-153.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0036_JOY_DR_CMH-153.raw
SUBJECT_SAMPLE_FACTORS           	-	87	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage	Sex=F; Age=72; Eye Collected=OS; Past Medical History=Diabetes Type 2, Hypertension; Medications=Lyrica, Coumadin, Furosemide, Pantoprazol, Metformin, Dilaudil, Bisoprolol, Ferrous sulfate, Lorazepan; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0037_JOY_VitHum_HIL-DR-87.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0037_JOY_DR_CMH-87.raw
SUBJECT_SAMPLE_FACTORS           	-	144	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage and cataract	Sex=F; Age=81; Eye Collected=OD; Past Medical History=Diabetes Type 2, Hypertension, Irondeficiency anaemia, dyslipidemia; Medications=Adalat, AAS, Docusate sodium, Metoprolol, Novolin, Furosemide, Ferrous sulfate; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=excluded; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0038_JOY_VitHum_HIL-DR-144.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0038_JOY_DR_CMH-144.raw
SUBJECT_SAMPLE_FACTORS           	-	77	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage	Sex=M; Age=73; Eye Collected=OS; Past Medical History=Diabetes Type 2; Medications=AAS, Atorvastatin, Metoprolol, Amlodipine, Oxybutynin, Tamsulosine, Januvia, Novolin, Gliclazide, Lorazepan, Nitro; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0039_JOY_VitHum_HIL-DR-77.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0039_JOY_DR_CMH-77.raw
SUBJECT_SAMPLE_FACTORS           	-	76	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage	Sex=M; Age=80; Eye Collected=OS; Past Medical History=Diabetes Type 2, Hypertension, Coronary artery disease; Medications=NA; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=-; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0040_JOY_VitHum_HIL-DR-76.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0040_JOY_DR_CMH-76.raw
SUBJECT_SAMPLE_FACTORS           	-	QC01	Sample source:pooled vitreous QC | Dianosis:NA | Disease Status:NA	Sex=NA; Age=NA; Eye Collected=NA; Past Medical History=NA; Medications=NA; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=NA; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0000g_JOY_VitHum_HIL-PREFB01.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0000d_JOY_VitHum_CMH_JP01.raw
SUBJECT_SAMPLE_FACTORS           	-	QC02	Sample source:pooled vitreous QC | Dianosis:NA | Disease Status:NA	Sex=NA; Age=NA; Eye Collected=NA; Past Medical History=NA; Medications=NA; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=NA; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0020b_JOY_VitHum_HIL-PREFB02.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0020a_JOY_VitHum_CMH_JP02.raw
SUBJECT_SAMPLE_FACTORS           	-	QC03	Sample source:pooled vitreous QC | Dianosis:NA | Disease Status:NA	Sex=NA; Age=NA; Eye Collected=NA; Past Medical History=NA; Medications=NA; Flagged as outlier in MetaboAnalyst Random Forest analysis (excluded)=NA; RAW_FILE_NAME(HILIC-pos_raw_file_name)=0040b_JOY_VitHum_HIL-PREFB03.raw; RAW_FILE_NAME(HILIC-neg_raw_file_name)=0040a_JOY_VitHum_CMH_JP03.raw
#COLLECTION
CO:COLLECTION_SUMMARY            	The study conforms to the tenets of the Declaration of Helsinki, and approval of
CO:COLLECTION_SUMMARY            	the human clinical protocol and informed consent were obtained from the
CO:COLLECTION_SUMMARY            	Maisonneuve-Rosemont Hospital Ethics Committee (CER: 10059). All patients
CO:COLLECTION_SUMMARY            	previously diagnosed with proliferative diabetic retinopathy or epiretinal
CO:COLLECTION_SUMMARY            	membrane were followed clinically, and surgery was performed by a single
CO:COLLECTION_SUMMARY            	vitreoretinal surgeon when indicated by 'standard-of-care' guidelines. Informed
CO:COLLECTION_SUMMARY            	consent was obtained. Undiluted vitreous samples were aspirated in the region
CO:COLLECTION_SUMMARY            	adjacent to neovascular tufts or epiretinal membrane (control) and were frozen
CO:COLLECTION_SUMMARY            	on dry ice immediately after biopsy and stored at –80°C. All patients
CO:COLLECTION_SUMMARY            	received their first anti-VEGF injection after vitreous sampling; they did not
CO:COLLECTION_SUMMARY            	have prior anti-VEGF or photocoagulation treatment. Medication details are
CO:COLLECTION_SUMMARY            	provided in the metadata table, except for four deceased diabetic patients whose
CO:COLLECTION_SUMMARY            	records were no longer available (NA). Sex and gender factors were not analyzed
CO:COLLECTION_SUMMARY            	due to insufficient statistical power when disaggregated.
CO:COLLECTION_PROTOCOL_ID        	CER: 10059
CO:SAMPLE_TYPE                   	Vitreous humor
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	No treatment was used in the study
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Samples were thawed on ice, vortexes, and aliquoted to prepare extracts for
SP:SAMPLEPREP_SUMMARY            	three different LC-MS methods: HILIC-pos: 10 µL of vitreous sample was
SP:SAMPLEPREP_SUMMARY            	extracted using 90 µL of acetonitrile/methanol/formic acid (74.9:24.9:0.2
SP:SAMPLEPREP_SUMMARY            	v/v/v) containing stable isotope-labeled internal standards (valine-d8,
SP:SAMPLEPREP_SUMMARY            	Sigma-Aldrich; St. Louis, MO; and phenylalanine-d8, Cambridge Isotope
SP:SAMPLEPREP_SUMMARY            	Laboratories; Andover, MA). The samples were centrifuged (10 min, 9,000 x g,
SP:SAMPLEPREP_SUMMARY            	4°C), and the supernatants were transferred to autosampler vials containing
SP:SAMPLEPREP_SUMMARY            	deactivated glass inserts. HILIC-neg: 30 µL of each vitreous sample was
SP:SAMPLEPREP_SUMMARY            	extracted using 120 µL of 80% methanol containing inosine-15N4, thymine-d4 and
SP:SAMPLEPREP_SUMMARY            	glycocholate-d4 internal standards (Cambridge Isotope Laboratories; Andover,
SP:SAMPLEPREP_SUMMARY            	MA). The samples were centrifuged (10 min, 9,000 x g, 4°C), and the
SP:SAMPLEPREP_SUMMARY            	supernatants were transferred to autosampler vials containing deactivated glass
SP:SAMPLEPREP_SUMMARY            	inserts.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	HILIC-neg: Hydrophilic interaction liquid chromatography (HILIC) analysis of
CH:CHROMATOGRAPHY_SUMMARY        	water soluble metabolites in the negative ionization mode
CH:CHROMATOGRAPHY_TYPE           	HILIC
CH:INSTRUMENT_NAME               	Shimadzu Nexera X2
CH:COLUMN_NAME                   	Phenomenex Luna NH2 (150 x 2 mm,5um,100Å)
CH:SOLVENT_A                     	100% water; 20 mM ammonium acetate; 20 mM ammonium hydroxide
CH:SOLVENT_B                     	75% methanol/25% acetonitrile; 10 mM ammonium hydroxide
CH:FLOW_GRADIENT                 	0-10 min, gradient from 90% B to 0% B; 10-12 min, isocratic 0% B; 12-14 min,
CH:FLOW_GRADIENT                 	gradient from 0% B to 90% B
CH:FLOW_RATE                     	400 uL/min
CH:COLUMN_TEMPERATURE            	30
#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                   	MS analyses were carried out using electrospray ionization in the negative ion
MS:MS_COMMENTS                   	mode using full scan analysis over m/z 70-750 at 70,000 resolution and 3 Hz data
MS:MS_COMMENTS                   	acquisition rate. Additional MS settings were: ion spray voltage, -3.0 kV;
MS:MS_COMMENTS                   	capillary temperature, 350°C; probe heater temperature, 325 °C; sheath gas,
MS:MS_COMMENTS                   	55; auxiliary gas, 10; and S-lens RF level 50. Raw data were processed using
MS:MS_COMMENTS                   	TraceFinder 4.1 software (Thermo Fisher Scientific; Waltham, MA) and Progenesis
MS:MS_COMMENTS                   	QI (Nonlinear Dynamics; Newcastle upon Tyne, UK). Metabolite identities were
MS:MS_COMMENTS                   	confirmed using authentic reference standards.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	peak areas
MS_METABOLITE_DATA_START
Samples	QC01	14	15	16	108	136	QC02	85	126	124	86	142	153	87	144	77	76	QC03
Factors	Sample source:pooled vitreous QC | Dianosis:NA | Disease Status:NA	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sample source:Vitreous humor | Dianosis:Epiretinal membrane (ERM) | Disease Status:Control	Sample source:pooled vitreous QC | Dianosis:NA | Disease Status:NA	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage and tractional retinal detachments	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with neovascular glaucoma	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage and tractional retinal detachments	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with tractional retinal detachments	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with macular edema and pre-retinal hemorrhage	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage and cataract	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage	Sample source:Vitreous humor | Dianosis:Proliferative diabetic retinopathy (PDR) | Disease Status:Active with vitreous hemorrhage	Sample source:pooled vitreous QC | Dianosis:NA | Disease Status:NA
thymine-d4	757591	736032	737870	720539	756598	783336	723075	669133	662413	679303	659163	745462	707949	707613	663888	660229	608413	722007
inosine-15N4	512664	465337	434370	503166	674065	509770	547413	629797	466346	593806	667465	552309	597162	739030	437596	737300	573404	537122
glycocholate-d4	166010	167793	171726	139550	151905	137940	142571	122874	149782	140135	110911	106750	150211	121519	130293	118836	110420	161258
2-aminoadipate									140116			118897						
2-furoylglycine															1181190	260467		
2-hydroxyglutarate	6908039	4655201	2507568	3972282	5848281	6257697	6115755	10661942	5897374	7096391	8933459	9296928	3716466	12187232	9864628	7537061	8483374	5683040
3-methyladipate/pimelate	3621931	3039336	2879050	3338109	3243267	3694492	2981655	3640911	2956793	2756307	3623916	4296923	3096537	2756032	3175558	3562356	2836757	2630082
4-hydroxymandelate	78255			22131				118604			178389	54900		155055	83170	127934	50291	
4-methylcatechol	624600	377920	486138	523362	300990	254328	454168	268762	348127	410932	373924	433100	1196606	307728	709622	465273	279140	396299
acetylalanine	4727882	4048314	988457	2893686	5115816	4597461	3511941	4645143	3922782	3639750	6512248	7151039	1074834	4417236	5134565	4692583	3424671	3601916
aconitate	143284230	53743790	25612519	53587263	146513800	141000637	178850303	66038201	89973454	154208083	71961786	277990408	361948474	72850662	225888997	94490882	92773750	183742800
alpha-hydroxybutyrate/beta-hydroxybutyrate	220381116	80652362	43649619	103665402	150324520	653316324	157364621	205373971	173858124	64408771	106480028	246055135	56965547	363012035	58246163	150687755	561986507	138325427
alpha-ketoglutarate	21219708	12852070	10534273	15162722	21541113	14781000	16397436	29807329	21792551	17402652	18426604	15898364	6582454	26119703	35468556	13885575	34220938	14453384
AMP								25574									421354	
caproate											1635828			298705				
dihydroorotate	170370			138395	50955	241334	47148	98126		61321	167935	251332		183576	94934	236060	118379	30860
gentisate	49678							278946				314721		120754	377942	230227	54153	
glutathione reduced	135499	343332	2494799	864990			60585											37601
glycerate	13129710	10924853	2927592	8771934	14340560	11666850	8744624	23967276	10987906	6563399	8938201	10881928	4075722	10784422	9101565	8550689	22384510	7937408
homogentisate	78255			22131				118604			178389	54900		155055	83170	127934	50291	
homovanillate	1153094	1517395	26808	801759	1682196	1995891	1056973	1282515	927870	978592	2267598	1823503	243431	1842718	1942542	1443889	2272473	830183
MDA	3139055	1929638	566572	2333900	2619125	3044817	2354638	6358045	2293546	2460186	2108591	2662725	1077989	2853659	2147624	2138707	4898970	2029496
methylmalonate	11596281	11477596	9057499	8315005	11154190	16204990	13475915	13859528	12888477	12834855	14722628	16713134	8470822	15204348	12502844	11158358	7659652	13310993
pentose monophosphate								29097			47682					184656		
pyruvate	518294066	410802913	167834664	210071384	380510657	575204182	325517742	409877409	337421600	255172685	129306344	204575918	129700290	143804480	261087215	165833465	271856938	202726718
sebacate	761755	619625	655864	741224	797513	776355	825378	949341	660578	759142	855599	955575	982042	724734	934474	747795	782979	769273
adipate	41573	45771	45439	45206	42157	50934	53870	45912	38003	40198	63244	67070	37860	49379	44300	40221	45842	48311
alpha-glycerophosphate	577	836	121	1416	1612	822	3038	5268	3061	9180	12315	6705	1403	1552	1608	4047	1755	2992
alpha-keto-beta-methylvalerate/alpha-ketoisocaproate	130802	86646	25578	88309	117971	247415	111188	214512	136687	132426	98739	171024	71673	231965	112006	211190	187440	107514
aspartate				796	260	201	1887	6713	680	1411	1487	17479	1397	1770	2233	3602	1537	1987
azelate	18227	25311	30104	30988	28893	29211	30846	31940	29851	31869	34322	33121	29990	31002	31398	35352	34667	30743
citrate	90082151	3972169	1835292	3178373	57761033	40836536	79173315	6766810	18559619	65487415	5417089	74690669	195852104	13228674	80997347	24079472	16986110	75585031
CMPF			77	15705		177361	13444	121537			1853			29995	6246	60559	424	12385
cystathionine						5397	203	2402			4402	9200		4247	11330			753
fructose/glucose/galactose	25219502	19658218	22648682	21091008	18750674	36639075	22472633	14452532	17275267	19229945	15594427	33087172	37963022	11156312	22773704	21608569	36081389	20866576
fucose	5104861	6127696	3272939	3755490	7245085	4366195	5092752	8599778	4719545	8997260	2126794	2553082	2096244	4642133	1016628	507639	2391240	5106504
fumarate/maleate	402548	295466	293474	332843	403394	349626	358289	401611	381083	341257	320303	365597	285344	378589	416250	331549	368546	348420
glucuronate	4610	3801	7635	24399	4080	25223	42366	130688	5478	43211	690659	626068	46243	151830	129091	224752	173400	54031
glutathione oxidized	230367	642076	3668033	1807050			224063											204616
hydrochlorothiazide	250				20655								23565					405
indoxylsulfate	681					1135	2666	12621			28090	14142	574	18540	20325	8930		1345
inositol	2541512	2908035	978520	1923957	3971862	2558462	2894252	3114694	3784221	2368250	3511930	3682547	1212474	2167611	7424044	2708214	3007490	3041181
isoleucine/leucine	3381542	2066120	1273718	2532017	2890417	3915223	3277532	4806675	5988737	6521982	3268211	4969996	1902385	2271170	1966419	3970632	3597270	3108948
lactate	11720045	7746939	3824710	7882723	9908310	11831171	8565920	11314478	9133530	8979008	8498255	10314704	5135330	10119066	8311327	8132445	9448718	7179280
malate	733153	401645	204802	438396	943354	513566	646758	816228	889352	682240	448933	781464	401590	911179	1083946	552195	784786	658983
malonate	57468	60702	63224	77198	66547	63854	62814	66934	65164	60336	62307	63579	55321	62331	65949	64835	67538	63302
methylcysteine	169					3862	657	969	8436	1953	4533		758			5056	4517	418
orotate	2807	482		2075	317	706												
oxalate	59039	1227	18949	35815	46919	62210	36109	169165	36513	58830	100456	276894	27543	121322	61359	103020	102253	46276
oxaloacetate	60386	769		520	37301	25839	52401	2963	11086	43743	1998	47079	130567	7660	52791	14505	9890	51139
pantothenate	405949	264709	124692	582009	314974	266133	314215	320675	453509	579756	600710	382541	64801	497948	434908	231395	342320	257703
quinate	48920	75197	5740	41515	24541	124613	36195	39474	19308	1637	72935	20193	910	35564	377938	305801	141431	29369
quinolinate	12450		2240	6973	7326	17499	14685	25611	7032	11719	80660	225194	3015	46186	21095	31043	25731	15044
ribothymidine	109541	92693	25074	74212	162010	135111	105515	141840	116365	107952	152340	134278	46548	130778	163569	95644	105698	95320
salicylurate							2486	50771				2937	12069		146254	57954	19003	2652
sorbitol	3781657	2529735	682111	2114544	4037036	4332225	3646748	2360146	3145246	2302907	4996840	5555048	1048224	3617339	5662808	1924675	2239225	3479660
suberate	70	4048	5563	7706	8909	7205	11225	8473	6769	8005	8353	10768	10699	5713	8179	5942	7690	7997
succinate	840738	620433	486989	759467	1534833	671043	988619	1366697	1205720	1032561	697144	773197	549793	1147317	1639075	599636	819089	913507
sucrose	203558	7616	110818	84817	48522	101677	251471	74596	4661	95702	436070	346446	135777	144612	301013	112548	228260	253164
thymine	43462	31019	13479	30106	46523	52363	39670	48897	39641	43373	77279	92055	18245	51867	69706	49020	47820	39770
uracil	112400	127949	55417	71493	182363	160833	106374	137637	138200	73421	105493	105298	62576	116310	65190	116761	92793	114454
urate	2198616	1454316	1212008	1717595	1157704	2821636	2271070	3400441	1261970	3399144	3985680	4482815	2120018	3970450	2348680	2860395	2958056	2150336
uridine	888074	1109697	428629	591539	1621494	1364880	919321	1191627	1127407	728213	852006	846409	453952	906630	532966	878919	739968	920251
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Compound_ID	MZ	RT	HMDB_ID (*representative)	mz_rt
thymine-d4	TF1	129.0608	1.30	internal standard	129.0608_1.3
inosine-15N4	TF2	271.0616	3.15	internal standard	271.0616_3.15
glycocholate-d4	TF3	468.3269	3.70	internal standard	468.3269_3.7
2-aminoadipate	TF4	160.0615	5.25	HMDB00510	160.0615_5.25
2-furoylglycine	TF5	168.0302	3.80	HMDB00439	168.0302_3.8
2-hydroxyglutarate	TF6	147.0299	7.00	HMDB59655*	147.0299_7
3-methyladipate/pimelate	TF7	159.0663	6.75	HMDB00555*	159.0663_6.75
4-hydroxymandelate	TF8	167.0350	4.60	HMDB00822	167.035_4.6
4-methylcatechol	TF9	123.0452	1.30	HMDB00873	123.0452_1.3
acetylalanine	TF10	130.0510	3.90	HMDB00766	130.051_3.9
aconitate	TF11	173.0092	9.10	HMDB00072*	173.0092_9.1
alpha-hydroxybutyrate/beta-hydroxybutyrate	TF12	103.0401	3.40	HMDB00008*	103.0401_3.4
alpha-ketoglutarate	TF13	145.0142	7.35	HMDB00208	145.0142_7.35
AMP	TF14	346.0558	7.65	HMDB00045	346.0558_7.65
caproate	TF15	115.0765	3.50	HMDB00535	115.0765_3.5
dihydroorotate	TF17	157.0255	4.10	HMDB03349	157.0255_4.1
gentisate	TF18	153.0193	4.60	HMDB00152	153.0193_4.6
glutathione reduced	TF19	306.0765	5.90	HMDB00125	306.0765_5.9
glycerate	TF20	105.0193	4.10	HMDB00139	105.0193_4.1
homogentisate	TF22	167.0340	4.60	HMDB00130	167.034_4.6
homovanillate	TF23	181.0506	4.40	HMDB00118	181.0506_4.4
MDA	TF25	71.0139	3.75	HMDB06112	71.0139_3.75
methylmalonate	TF26	117.0193	7.10	HMDB00202	117.0193_7.1
pentose monophosphate	TF27	229.0119	7.25	HMDB01548*	229.0119_7.25
pyruvate	TF28	87.0088	4.80	HMDB00243	87.0088_4.8
sebacate	TF29	201.1132	6.75	HMDB00792	201.1132_6.75
adipate	QI2	145.0506	6.80	HMDB00448	145.0506_6.8
alpha-glycerophosphate	QI4	171.0064	7.25	HMDB00126	171.0064_7.25
alpha-keto-beta-methylvalerate/alpha-ketoisocaproate	QI5	129.0557	3.40	HMDB00491*	129.0557_3.4
aspartate	QI8	132.0302	5.25	HMDB00191	132.0302_5.25
azelate	QI9	187.0976	6.95	HMDB00784	187.0976_6.95
citrate	QI10	191.0197	9.00	HMDB00094	191.0197_9
CMPF	QI12	239.0925	7.40	HMDB61112	239.0925_7.4
cystathionine	QI13	221.0602	5.35	HMDB00099	221.0602_5.35
fructose/glucose/galactose	QI14	179.0561	1.85	HMDB00122*	179.0561_1.85
fucose	QI15	163.0612	1.40	HMDB00174	163.0612_1.4
fumarate/maleate	QI16	115.0037	7.05	HMDB00134*	115.0037_7.05
glucuronate	QI17	193.0354	5.00	HMDB00127	193.0354_5
glutathione oxidized	QI20	611.1447	7.80	HMDB03337	611.1447_7.8
hydrochlorothiazide	QI24	179.0350	4.65	HMDB01928	179.035_4.65
indoxylsulfate	QI26	212.0023	3.80	HMDB00682	212.0023_3.8
inositol	QI27	179.0561	2.70	HMDB00211	179.0561_2.7
isoleucine/leucine	QI28	130.0870	2.50	HMDB00172*	130.087_2.5
lactate	QI29	89.0244	3.85	HMDB00190	89.0244_3.85
malate	QI31	133.0142	6.95	HMDB00156	133.0142_6.95
malonate	QI32	103.0037	5.00	HMDB00691	103.0037_5
methylcysteine	QI34	134.0281	3.45	HMDB02108	134.0281_3.45
orotate	QI36	155.0098	4.50	HMDB00226	155.0098_4.5
oxalate	QI37	88.9880	7.40	HMDB02329	88.988_7.4
oxaloacetate	QI38	130.9990	1.00	HMDB00223	130.999_1
pantothenate	QI39	218.1034	3.90	HMDB00210	218.1034_3.9
quinate	QI42	191.0561	4.30	HMDB03072	191.0561_4.3
quinolinate	QI43	166.0146	7.45	HMDB00232	166.0146_7.45
ribothymidine	QI44	257.0779	1.55	HMDB00884	257.0779_1.55
salicylurate	QI45	194.0459	6.10	HMDB00840	194.0459_6.1
sorbitol	QI47	181.0718	2.00	HMDB00247	181.0718_2
suberate	QI48	173.0819	6.75	HMDB00893	173.0819_6.75
succinate	QI49	117.0193	6.90	HMDB00254	117.0193_6.9
sucrose	QI50	341.1080	2.20	HMDB00258	341.108_2.2
thymine	QI53	125.0357	1.35	HMDB00262	125.0357_1.35
uracil	QI56	111.0200	1.50	HMDB00300	111.02_1.5
urate	QI57	167.0211	5.25	HMDB00289	167.0211_5.25
uridine	QI58	243.0623	1.75	HMDB00296	243.0623_1.75
METABOLITES_END
#END