#METABOLOMICS WORKBENCH KasparasP_20240820_021723 DATATRACK_ID:5125 STUDY_ID:ST003418 ANALYSIS_ID:AN005617 PROJECT_ID:PR002115
VERSION             	1
CREATED_ON             	August 20, 2024, 4:02 am
#PROJECT
PR:PROJECT_TITLE                 	TRAM–LAG1–CLN8 family proteins are acyltransferases regulating phospholipid
PR:PROJECT_TITLE                 	composition
PR:PROJECT_SUMMARY               	The diversity of cellular phospholipids, crucial for membrane homeostasis and
PR:PROJECT_SUMMARY               	function, arises from enzymatic remodeling of their fatty acyl chains. In this
PR:PROJECT_SUMMARY               	work, we reveal that poorly understood TRAM–LAG1–CLN8 domain-containing
PR:PROJECT_SUMMARY               	(TLCD) proteins are phospholipid remodeling enzymes. We demonstrate that TLCD1
PR:PROJECT_SUMMARY               	is an evolutionarily conserved lysophosphatidylethanolamine acyltransferase,
PR:PROJECT_SUMMARY               	which regulates cellular phospholipid composition and generates novel fatty acid
PR:PROJECT_SUMMARY               	and thiamine (vitamin B1) esters as its secondary products. Furthermore, we
PR:PROJECT_SUMMARY               	establish that human TLCD protein CLN8, mutations in which cause fatal
PR:PROJECT_SUMMARY               	neurodegenerative Batten disease, is a lysophosphatidylglycerol acyltransferase.
PR:PROJECT_SUMMARY               	We show that CLN8 catalyzes the essential step in the biosynthesis of
PR:PROJECT_SUMMARY               	bis(monoacylglycero)phosphate, a phospholipid critical for lysosome function.
PR:PROJECT_SUMMARY               	Our study unveils a new family of acyltransferases integral to cellular membrane
PR:PROJECT_SUMMARY               	phospholipid homeostasis and human disease.
PR:INSTITUTE                     	University of Cambridge
PR:LAST_NAME                     	Petkevicius
PR:FIRST_NAME                    	Kasparas
PR:ADDRESS                       	The Keith Peters Building, Cambridge, Cambridgeshire, CB2 0XY, United Kingdom
PR:EMAIL                         	kp416@mrc-mbu.cam.ac.uk
PR:PHONE                         	+447500233355
PR:PUBLICATIONS                  	TRAM–LAG1–CLN8 family proteins are acyltransferases regulating phospholipid
PR:PUBLICATIONS                  	composition
#STUDY
ST:STUDY_TITLE                   	Analysis of lipid composition of TLCD1 KO cultured cells
ST:STUDY_SUMMARY                 	Untargeted lipidomics experiments were conducted to analyze the differences in
ST:STUDY_SUMMARY                 	lipid composition between TLCD1 KO and isogenic control HeLa and U2OS cell
ST:STUDY_SUMMARY                 	lines. See a reference publication (Sheokand et al) for details.
ST:INSTITUTE                     	University of Cambridge
ST:LAST_NAME                     	Petkevicius
ST:FIRST_NAME                    	Kasparas
ST:ADDRESS                       	The Keith Peters Building
ST:EMAIL                         	kp416@mrc-mbu.cam.ac.uk
ST:PHONE                         	07500233355
#SUBJECT
SU:SUBJECT_TYPE                  	Cultured cells
SU:SUBJECT_SPECIES               	Homo sapiens
SU:TAXONOMY_ID                   	9606
#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           	-	Cell process blank	Genotype:Process blank | Sample source:Process blank | Clonality:Process blank | Replicate:Process blank	RAW_FILE_NAME(Raw file name)=Cell_process_blank.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa Wild-Type poolReplicate 1	Genotype:Wild-type | Sample source:HeLa | Clonality:Cell pool | Replicate:1	RAW_FILE_NAME(Raw file name)=HeLa_Wild-Type_pool_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa Wild-Type poolReplicate 2	Genotype:Wild-type | Sample source:HeLa | Clonality:Cell pool | Replicate:2	RAW_FILE_NAME(Raw file name)=HeLa_Wild-Type_pool_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa WildType poolReplicate 3	Genotype:Wild-type | Sample source:HeLa | Clonality:Cell pool | Replicate:3	RAW_FILE_NAME(Raw file name)=HeLa_Wild-Type_pool_Replicate_3.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa TLCD1 KO poolReplicate 1	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Cell pool | Replicate:1	RAW_FILE_NAME(Raw file name)=HeLa_TLCD1_KO_pool_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa TLCD1 KO poolReplicate 2	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Cell pool | Replicate:2	RAW_FILE_NAME(Raw file name)=HeLa_TLCD1_KO_pool_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa TLCD1 KO poolReplicate 3	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Cell pool | Replicate:3	RAW_FILE_NAME(Raw file name)=HeLa_TLCD1_KO_pool_Replicate_3.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa WildType clone 1Replicate 1	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:1	RAW_FILE_NAME(Raw file name)=HeLa_Wild-Type_clone_1_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa Wild-Type clone 1Replicate 2	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:2	RAW_FILE_NAME(Raw file name)=HeLa_Wild-Type_clone_1_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa Wild-Type clone 1Replicate 3	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:3	RAW_FILE_NAME(Raw file name)=HeLa_Wild-Type_clone_1_Replicate_3.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa Wild-Type clone 2Replicate 1	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:1	RAW_FILE_NAME(Raw file name)=HeLa_Wild-Type_clone_2_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa WildType clone 2Replicate 2	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:2	RAW_FILE_NAME(Raw file name)=HeLa_Wild-Type_clone_2_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa Wild-Type clone 2Replicate 3	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:3	RAW_FILE_NAME(Raw file name)=HeLa_Wild-Type_clone_2_Replicate_3.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa TLCD1 KO cloneReplicate 1	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Clone derived | Replicate:1	RAW_FILE_NAME(Raw file name)=HeLa_TLCD1_KO_clone_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa TLCD1 KO cloneReplicate 2	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Clone derived | Replicate:2	RAW_FILE_NAME(Raw file name)=HeLa_TLCD1_KO_clone_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	HeLa TLCD1 KO cloneReplicate 3	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Clone derived | Replicate:3	RAW_FILE_NAME(Raw file name)=HeLa_TLCD1_KO_clone_Replicate_3.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S WildType poolReplicate 1	Genotype:Wild-type | Sample source:U2OS | Clonality:Cell pool | Replicate:1	RAW_FILE_NAME(Raw file name)=U20S_Wild-Type_pool_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S Wild-Type poolReplicate 2	Genotype:Wild-type | Sample source:U2OS | Clonality:Cell pool | Replicate:2	RAW_FILE_NAME(Raw file name)=U20S_Wild-Type_pool_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S Wild-Type poolReplicate 3	Genotype:Wild-type | Sample source:U2OS | Clonality:Cell pool | Replicate:3	RAW_FILE_NAME(Raw file name)=U20S_Wild-Type_pool_Replicate_3.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S TLCD1 KO poolReplicate 1	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Cell pool | Replicate:1	RAW_FILE_NAME(Raw file name)=U20S_TLCD1_KO_pool_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S TLCD1 KO poolReplicate 2	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Cell pool | Replicate:2	RAW_FILE_NAME(Raw file name)=U20S_TLCD1_KO_pool_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S TLCD1 KO poolReplicate 3	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Cell pool | Replicate:3	RAW_FILE_NAME(Raw file name)=U20S_TLCD1_KO_pool_Replicate_3.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S Wild-Type clone 1Replicate 1	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:1	RAW_FILE_NAME(Raw file name)=U20S_Wild-Type_clone_1_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S Wild-Type clone 1Replicate 2	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:2	RAW_FILE_NAME(Raw file name)=U20S_Wild-Type_clone_1_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S Wild-Type clone 1Replicate 3	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:3	RAW_FILE_NAME(Raw file name)=U20S_Wild-Type_clone_1_Replicate_3.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S Wild-Type clone 2Replicate 1	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:1	RAW_FILE_NAME(Raw file name)=U20S_Wild-Type_clone_2_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S Wild-Type clone 2Replicate 2	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:2	RAW_FILE_NAME(Raw file name)=U20S_Wild-Type_clone_2_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S Wild-Type clone 2Replicate 3	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:3	RAW_FILE_NAME(Raw file name)=U20S_Wild-Type_clone_2_Replicate_3.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S TLCD1 KO cloneReplicate 1	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Clone derived | Replicate:1	RAW_FILE_NAME(Raw file name)=U20S_TLCD1_KO_clone_Replicate_1.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S TLCD1 KO cloneReplicate 2	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Clone derived | Replicate:2	RAW_FILE_NAME(Raw file name)=U20S_TLCD1_KO_clone_Replicate_2.raw
SUBJECT_SAMPLE_FACTORS           	-	U20S TLCD1 KO cloneReplicate 3	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Clone derived | Replicate:3	RAW_FILE_NAME(Raw file name)=U20S_TLCD1_KO_clone_Replicate_3.raw
#COLLECTION
CO:COLLECTION_SUMMARY            	All cell lines were maintained in Dulbecco’s Modified Eagle Medium (DMEM,
CO:COLLECTION_SUMMARY            	11965084, Thermo Fisher) supplemented with 10% fetal bovine serum (FBS, Sigma)
CO:COLLECTION_SUMMARY            	at 37°C and 5% CO2. To collect samples for lipid measurements, confluent cells
CO:COLLECTION_SUMMARY            	in 6-well plates were swiftly washed twice with 3 ml of ice-cold PBS on ice,
CO:COLLECTION_SUMMARY            	then scraped into 500 μl of ice-cold PBS on ice using inverted 200 μl pipette
CO:COLLECTION_SUMMARY            	tip. The resulting cell suspension was transferred into pre-chilled 2 ml plastic
CO:COLLECTION_SUMMARY            	vials used for lipid extraction (3469-11, Thermo Scientific), and centrifuged at
CO:COLLECTION_SUMMARY            	500 g, 4°C for 5 min. The supernatant was aspirated and the cell pellet was
CO:COLLECTION_SUMMARY            	snap-frozen and stored at -70°C. One well of a 6-well plate yielded one
CO:COLLECTION_SUMMARY            	replicate in analysis.
CO:SAMPLE_TYPE                   	Cultured cells
CO:STORAGE_CONDITIONS            	-80℃
#TREATMENT
TR:TREATMENT_SUMMARY             	Cells were untreated (collected under standard culturing conditions).
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	The extraction of total lipids from cellular matrices, immunoprecipitated
SP:SAMPLEPREP_SUMMARY            	mitochondria and in vitro assays was conducted employing the butanol-methanol
SP:SAMPLEPREP_SUMMARY            	(BUME) method, as described in detail (37). Note that the chloroform-methanol
SP:SAMPLEPREP_SUMMARY            	lipid extraction methods result in the partitioning of acyl-thiamines into the
SP:SAMPLEPREP_SUMMARY            	polar phase. 2 ml screw cap plastic tubes were used (3469-11, Thermo
SP:SAMPLEPREP_SUMMARY            	Scientific), and a blank extraction was always performed in parallel to account
SP:SAMPLEPREP_SUMMARY            	for the plastic-related contaminants. The extraction commenced with the
SP:SAMPLEPREP_SUMMARY            	homogenization of frozen cell pellets, mitochondrial beads or in vitro assay
SP:SAMPLEPREP_SUMMARY            	mixtures in a 0.5 ml ice-cold solution of butanol to methanol in a 3:1 ratio.
SP:SAMPLEPREP_SUMMARY            	For lipidomics samples, BUME solution was enriched with SPLASH internal standard
SP:SAMPLEPREP_SUMMARY            	mix (330707, Avanti Polar Lipids). For the extraction, a further 0.5 ml of 1%
SP:SAMPLEPREP_SUMMARY            	acetic acid and 0.5 ml of a heptane:ethyl acetate 3:1 mixture were added,
SP:SAMPLEPREP_SUMMARY            	followed by vigorous vortexing for a total of 5 minutes. The mixture was then
SP:SAMPLEPREP_SUMMARY            	centrifuged at 6000 g for 5 minutes, allowing for the separation of phases,
SP:SAMPLEPREP_SUMMARY            	after which the upper organic phase was carefully decanted into glass vials. A
SP:SAMPLEPREP_SUMMARY            	second extraction was conducted on the remaining aqueous phase, with the newly
SP:SAMPLEPREP_SUMMARY            	acquired upper phase being combined in the same glass vials as the first. Post
SP:SAMPLEPREP_SUMMARY            	extraction, the solvents were evaporated under a stream of nitrogen, and the
SP:SAMPLEPREP_SUMMARY            	resultant dry lipid extracts were preserved at −70°C pending further
SP:SAMPLEPREP_SUMMARY            	analysis.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Dried samples were reconstituted in 100 μL of isopropanol, acetonitrile, and
CH:CHROMATOGRAPHY_SUMMARY        	water (2:1:1 ratio) and thoroughly vortexed. Liquid chromatography was conducted
CH:CHROMATOGRAPHY_SUMMARY        	using a Shimadzu HPLC System, with 10 μL of the sample introduced onto a Waters
CH:CHROMATOGRAPHY_SUMMARY        	Acquity Premier UPLC® CSH column (1.7 μm pore size, 2.1 mm × 50 mm), which
CH:CHROMATOGRAPHY_SUMMARY        	was maintained at 55 °C. The mobile phase A comprised a 6:4 ratio of
CH:CHROMATOGRAPHY_SUMMARY        	acetonitrile to water with 10 mM ammonium formate, and mobile phase B consisted
CH:CHROMATOGRAPHY_SUMMARY        	of a 9:1 ratio of isopropanol to acetonitrile with 10 mM ammonium formate. A
CH:CHROMATOGRAPHY_SUMMARY        	flow rate of 500 μL per minute was maintained with a gradient protocol for
CH:CHROMATOGRAPHY_SUMMARY        	mobile phase B as follows: 0.00 minutes_40% mobile phase B; 1.5 minutes_40%
CH:CHROMATOGRAPHY_SUMMARY        	mobile phase B; 8.00 minutes_99% mobile phase B; 10.00 minutes_99% mobile phase
CH:CHROMATOGRAPHY_SUMMARY        	B; 10.10 minutes_40% mobile phase B; 12.00 minutes_40% mobile phase. The sample
CH:CHROMATOGRAPHY_SUMMARY        	injection needle was rinsed with a 9:1 isopropanol and acetonitrile solution
CH:CHROMATOGRAPHY_SUMMARY        	(strong wash) and isopropanol, acetonitrile, and water (2:1:1, weak wash).
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Waters Acquity
CH:COLUMN_NAME                   	Waters ACQUITY UPLC CSH C18 (100 x 2.1mm,1.7um)
CH:SOLVENT_A                     	6:4 of acetonitrile to water with 10 mM ammonium formate
CH:SOLVENT_B                     	9:1 of isopropanol to acetonitrile with 10 mM ammonium formate
CH:FLOW_GRADIENT                 	Gradient protocol for mobile phase B as follows: 0.00 minutes_40% mobile phase
CH:FLOW_GRADIENT                 	B; 1.5 minutes_40% mobile phase B; 8.00 minutes_99% mobile phase B; 10.00
CH:FLOW_GRADIENT                 	minutes_99% mobile phase B; 10.10 minutes_40% mobile phase B; 12.00 minutes_40%
CH:FLOW_GRADIENT                 	mobile phase.
CH:FLOW_RATE                     	500 μL per minute
CH:COLUMN_TEMPERATURE            	55
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Q Exactive Orbitrap
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	UNSPECIFIED
MS:MS_COMMENTS                   	Mass spectrometric detection was carried out on a ThermoFisher Scientific
MS:MS_COMMENTS                   	Q-Exactive Orbitrap equipped with a heated electrospray ionization source. The
MS:MS_COMMENTS                   	mass spectrometer was calibrated immediately before sample analysis using
MS:MS_COMMENTS                   	positive and negative ionization calibration solution (recommended by Thermo
MS:MS_COMMENTS                   	Scientific). The electrospray ionization parameters were optimized with a 50:50
MS:MS_COMMENTS                   	mix of mobile phase A and B for spray stability, setting the capillary
MS:MS_COMMENTS                   	temperature at 300 °C, source heater temperature at 420 °C, with the sheath,
MS:MS_COMMENTS                   	auxiliary, and spare gas flows at specific arbitrary units (40, 15 and 3,
MS:MS_COMMENTS                   	respectively), and source voltage at 4 kV. The mass spectrometer operated at a
MS:MS_COMMENTS                   	scan rate of 4 Hz, yielding a resolution of 35,000 at m/z 200, over a full-scan
MS:MS_COMMENTS                   	range from m/z 120 to 1800, with continuous switching between positive and
MS:MS_COMMENTS                   	negative modes.
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	nmol
MS_METABOLITE_DATA_START
Samples	Cell process blank	HeLa Wild-Type poolReplicate 1	HeLa Wild-Type poolReplicate 2	HeLa WildType poolReplicate 3	HeLa TLCD1 KO poolReplicate 1	HeLa TLCD1 KO poolReplicate 2	HeLa TLCD1 KO poolReplicate 3	HeLa WildType clone 1Replicate 1	HeLa Wild-Type clone 1Replicate 2	HeLa Wild-Type clone 1Replicate 3	HeLa Wild-Type clone 2Replicate 1	HeLa WildType clone 2Replicate 2	HeLa Wild-Type clone 2Replicate 3	HeLa TLCD1 KO cloneReplicate 1	HeLa TLCD1 KO cloneReplicate 2	HeLa TLCD1 KO cloneReplicate 3	U20S WildType poolReplicate 1	U20S Wild-Type poolReplicate 2	U20S Wild-Type poolReplicate 3	U20S TLCD1 KO poolReplicate 1	U20S TLCD1 KO poolReplicate 2	U20S TLCD1 KO poolReplicate 3	U20S Wild-Type clone 1Replicate 1	U20S Wild-Type clone 1Replicate 2	U20S Wild-Type clone 1Replicate 3	U20S Wild-Type clone 2Replicate 1	U20S Wild-Type clone 2Replicate 2	U20S Wild-Type clone 2Replicate 3	U20S TLCD1 KO cloneReplicate 1	U20S TLCD1 KO cloneReplicate 2	U20S TLCD1 KO cloneReplicate 3
Factors	Genotype:Process blank | Sample source:Process blank | Clonality:Process blank | Replicate:Process blank	Genotype:Wild-type | Sample source:HeLa | Clonality:Cell pool | Replicate:1	Genotype:Wild-type | Sample source:HeLa | Clonality:Cell pool | Replicate:2	Genotype:Wild-type | Sample source:HeLa | Clonality:Cell pool | Replicate:3	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Cell pool | Replicate:1	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Cell pool | Replicate:2	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Cell pool | Replicate:3	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:1	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:2	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:3	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:1	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:2	Genotype:Wild-type | Sample source:HeLa | Clonality:Clone derived | Replicate:3	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Clone derived | Replicate:1	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Clone derived | Replicate:2	Genotype:TLCD1 KO | Sample source:HeLa | Clonality:Clone derived | Replicate:3	Genotype:Wild-type | Sample source:U2OS | Clonality:Cell pool | Replicate:1	Genotype:Wild-type | Sample source:U2OS | Clonality:Cell pool | Replicate:2	Genotype:Wild-type | Sample source:U2OS | Clonality:Cell pool | Replicate:3	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Cell pool | Replicate:1	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Cell pool | Replicate:2	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Cell pool | Replicate:3	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:1	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:2	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:3	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:1	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:2	Genotype:Wild-type | Sample source:U2OS | Clonality:Clone derived | Replicate:3	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Clone derived | Replicate:1	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Clone derived | Replicate:2	Genotype:TLCD1 KO | Sample source:U2OS | Clonality:Clone derived | Replicate:3
PE_(34:1)	1022823	0.187901734	0.145045452	0.201884295	0.121710297	0.148609138	0.163156933	0.227184022	0.215303936	0.224973072	0.220915227	0.284269637	0.277423322	0.101066772	0.085050763	0.08621723	0.249174314	0.171312194	0.217500263	0.2425762	0.293209339	0.28081422	0.195599689	0.192477413	0.16861707	0.209711903	0.180160925	0.224548606	0.145048647	0.211907038	0.194254151
PE_(34:2)	0	0.018576298	0.021360159	0.029232169	0.007429292	0.009259734	0.008344382	0.033624231	0.034483564	0.03479247	0.04161393	0.047953093	0.042160136	0.00196992	0.001721508	0.001560944	0.043738298	0.034853305	0.041869307	0.022901036	0.027021184	0.021983773	0.027696697	0.031449308	0.026062347	0.032907673	0.02940544	0.034139336	0.009068567	0.005561351	0.015383424
PE_(35:1)	272498	0.03392432	0.030257486	0.036468866	0.027121343	0.032579222	0.033892533	0.047710614	0.046697203	0.04752163	0.038514969	0.041126654	0.036866298	0.02759117	0.024937862	0.023933166	0.037023057	0.024234244	0.032710238	0.039920641	0.04301159	0.041281647	0.037610453	0.03731011	0.033115758	0.031860189	0.024684524	0.030116346	0.035252438	0.047438814	0.04492636
PE_(36:1)	1536460	0.381565058	0.322105288	0.408133661	0.332517851	0.367599103	0.440286673	0.54839163	0.496553575	0.51432126	0.444121541	0.426000296	0.428511383	0.397191549	0.330619561	0.335062206	0.306136755	0.193853174	0.25475438	0.370095943	0.399737786	0.457465543	0.326154728	0.321833041	0.290190295	0.324060585	0.23672395	0.30730953	0.27546516	0.39113438	0.347736357
PE_(36:2)	650733	0.254421712	0.229013588	0.265373222	0.146610845	0.161508418	0.164420109	0.32622425	0.328835838	0.316917438	0.306245994	0.328014362	0.321166626	0.081594233	0.060050969	0.061846993	0.277856931	0.204486278	0.246090334	0.190957975	0.209655371	0.207343296	0.275244115	0.272814421	0.249452773	0.223300489	0.192612162	0.234431927	0.100841801	0.143412525	0.198162178
PE_(36:3)	0	0.013242189	0.011386534	0.008631244	0.006520997	0.006705991	0.007991754	0.013540787	0.009073252	0.007521008	0.011913573	0.012840785	0.011234469	0.001430165	0.001737679	0.001379733	0.029588736	0.018813537	0.023070661	0.021755772	0.023630543	0.024187214	0.02056614	0.024223742	0.019336888	0.023953012	0.018891364	0.020970933	0.013471995	0.019160092	0.01941333
PE_(36:4)	108448	0.098675606	0.086852834	0.115249431	0.084316503	0.088692033	0.09617645	0.110089835	0.101573367	0.106655852	0.103158977	0.118147713	0.101715319	0.061266149	0.050209852	0.046297808	0.110139128	0.089181207	0.100620073	0.12014884	0.135639644	0.130485071	0.116148093	0.116743121	0.096053667	0.105333842	0.091215439	0.107616636	0.078706092	0.131025732	0.124401807
PE_(36:5)	0	0.029752244	0.025020508	0.034580699	0.009459883	0.010408392	0.013476884	0.03548983	0.034811272	0.037560496	0.032416618	0.0327764	0.034477074	0.005581015	0.005285744	0.004588553	0.043267488	0.030461982	0.039286878	0.016675715	0.018396025	0.020012868	0.037933622	0.038957826	0.035714486	0.03819488	0.034162421	0.041593013	0.005306083	0.006863041	0.004926828
PE_(38:3)	577818	0.051907505	0.04445581	0.054800028	0.041070697	0.047389536	0.049145993	0.060591444	0.062682934	0.057191951	0.060800089	0.066205966	0.056907762	0.023202463	0.021858708	0.019876429	0.085985494	0.059715753	0.078316595	0.083615072	0.092889335	0.085879602	0.089852994	0.087791743	0.078091995	0.100952303	0.080055813	0.092160441	0.088333159	0.11187958	0.108737619
PE_(38:4)	3200829	0.434175245	0.377441019	0.443370263	0.446195272	0.474359652	0.518613302	0.456643278	0.458667297	0.456517782	0.353360167	0.365351587	0.352110601	0.429985037	0.377600625	0.343058031	0.471473247	0.353944751	0.419104152	0.570428964	0.610278342	0.611553291	0.519131714	0.523134099	0.474948594	0.468232247	0.422827422	0.514572079	0.490849031	0.670600783	0.642611516
PE_(38:5)	0	0.120790615	0.09944068	0.11940586	0.055139892	0.069485408	0.069034835	0.1464627	0.141375402	0.130016357	0.140481364	0.146504362	0.132218098	0.033140331	0.031302044	0.026472523	0.118868888	0.088279992	0.099306427	0.077759946	0.080374011	0.083713038	0.109117685	0.121000341	0.101139732	0.093616604	0.083082828	0.101610902	0.038249148	0.063712982	0.059589718
PE_(38:6)	13043	0.061843457	0.052660812	0.060190642	0.038969007	0.04492237	0.053974707	0.066030571	0.069078255	0.069688517	0.070568477	0.072004059	0.068522475	0.01604715	0.017494728	0.014199032	0.017140986	0.01249462	0.015932785	0.01887232	0.020865083	0.019252194	0.020398069	0.021169293	0.020589508	0.015236297	0.012668607	0.015338109	0.013674158	0.022581015	0.020252755
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	m/z [M+H]+	Average Rt(min)
PE_(34:1)	718.54004	4.781
PE_(34:2)	716.52209	4.303
PE_(35:1)	732.55115	5.03
PE_(36:1)	746.56958	5.243
PE_(36:2)	744.552	4.827
PE_(36:3)	742.5318	4.526
PE_(36:4)	740.52222	4.294
PE_(36:5)	738.50513	3.708
PE_(38:3)	770.56818	5.035
PE_(38:4)	768.55334	4.836
PE_(38:5)	766.53131	4.346
PE_(38:6)	764.52179	4.145
METABOLITES_END
#END