#METABOLOMICS WORKBENCH Giovanni_DAngelo_20210129_041443 DATATRACK_ID:2433 STUDY_ID:ST001672 ANALYSIS_ID:AN002730
VERSION                          	1
CREATED_ON                       	03-03-2022
#PROJECT
PR:PROJECT_TITLE                 	Targeted Sphingolipid analysis of human Fibroblasts silenced for or
PR:PROJECT_TITLE                 	overexpressing GOLPH3
PR:PROJECT_SUMMARY               	A group of sequentially-acting enzymes operating at the branchpoint among
PR:PROJECT_SUMMARY               	sphingolipid synthetic pathways binds the Golgi-localised oncoprotein GOLPH3.
PR:PROJECT_SUMMARY               	GOLPH3 sorts these enzymes into vesicles for intra-Golgi retro-transport, acting
PR:PROJECT_SUMMARY               	as a component of the cisternae inter-conversion mechanisms. Through these
PR:PROJECT_SUMMARY               	effects, GOLPH3 controls the sub-Golgi localisation, and the lysosomal
PR:PROJECT_SUMMARY               	degradation rate of specific enzymes. Here we evaluated the impact of
PR:PROJECT_SUMMARY               	overexpressing or silencing GOLPH3 on the sphingolipid composition of dermal
PR:PROJECT_SUMMARY               	human fibroblasts by targeted lipid analysis.
PR:INSTITUTE                     	École polytechnique fédérale de Lausanne (EPFL)
PR:DEPARTMENT                    	IBI
PR:LABORATORY                    	UPDANGELO
PR:LAST_NAME                     	D'Angelo
PR:FIRST_NAME                    	Giovanni
PR:ADDRESS                       	Station 15 CH1015 Lausanne Switzerland
PR:EMAIL                         	giovanni.dangelo@epfl.ch
PR:PHONE                         	+41 216934276
PR:DOI                           	http://dx.doi.org/10.21228/M8R97G
#STUDY
ST:STUDY_TITLE                   	Targeted Sphingolipid analysis of human Fibroblasts silenced for or
ST:STUDY_TITLE                   	overexpressing GOLPH3 (part-I)
ST:STUDY_SUMMARY                 	A group of sequentially-acting enzymes operating at the branchpoint among
ST:STUDY_SUMMARY                 	sphingolipid synthetic pathways binds the Golgi-localised oncoprotein GOLPH3.
ST:STUDY_SUMMARY                 	GOLPH3 sorts these enzymes into vesicles for intra-Golgi retro-transport, acting
ST:STUDY_SUMMARY                 	as a component of the cisternae inter-conversion mechanisms. Through these
ST:STUDY_SUMMARY                 	effects, GOLPH3 controls the sub-Golgi localisation, and the lysosomal
ST:STUDY_SUMMARY                 	degradation rate of specific enzymes. Here we evaluated the impact of
ST:STUDY_SUMMARY                 	overexpressing or silencing GOLPH3 on the sphingolipid composition of dermal
ST:STUDY_SUMMARY                 	human fibroblasts by targeted lipid analysis.
ST:INSTITUTE                     	École polytechnique fédérale de Lausanne (EPFL)
ST:DEPARTMENT                    	IBI
ST:LABORATORY                    	UPDANGELO
ST:LAST_NAME                     	D'Angelo
ST:FIRST_NAME                    	Giovanni
ST:ADDRESS                       	Station 15 CH1015 Lausanne Switzerland
ST:EMAIL                         	giovanni.dangelo@epfl.ch
ST:PHONE                         	+41 216934276
ST:SUBMIT_DATE                   	2021-01-29
#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]Additional sample data
SUBJECT_SAMPLE_FACTORS           	-	GOLPH3_OE_1	Treatment:GOLPH3 overexpression	RAW_FILE_NAME=GOLPH3_OE_1.raw
SUBJECT_SAMPLE_FACTORS           	-	GOLPH3_OE_2	Treatment:GOLPH3 overexpression	RAW_FILE_NAME=GOLPH3_OE_2.raw
SUBJECT_SAMPLE_FACTORS           	-	GOLPH3_OE_3	Treatment:GOLPH3 overexpression	RAW_FILE_NAME=GOLPH3_OE_3.raw
SUBJECT_SAMPLE_FACTORS           	-	GOLPH3_KD_1	Treatment:GOLPH3 silencing	RAW_FILE_NAME=GOLPH3_KD_1.raw
SUBJECT_SAMPLE_FACTORS           	-	GOLPH3_KD_2	Treatment:GOLPH3 silencing	RAW_FILE_NAME=GOLPH3_KD_2.raw
SUBJECT_SAMPLE_FACTORS           	-	GOLPH3_KD_3	Treatment:GOLPH3 silencing	RAW_FILE_NAME=GOLPH3_KD_3.raw
SUBJECT_SAMPLE_FACTORS           	-	CTRL_1	Treatment:no treatment	RAW_FILE_NAME=CTRL_1.raw
SUBJECT_SAMPLE_FACTORS           	-	CTRL_2	Treatment:no treatment	RAW_FILE_NAME=CTRL_2.raw
SUBJECT_SAMPLE_FACTORS           	-	CTRL_3	Treatment:no treatment	RAW_FILE_NAME=CTRL_3.raw
#COLLECTION
CO:COLLECTION_SUMMARY            	Cells were washed with ice cold PBS and draped
CO:SAMPLE_TYPE                   	Fibroblasts
#TREATMENT
TR:TREATMENT_SUMMARY             	Cells were either infected adenoviruses encoding GOLPH3 or treated with siRNAs
TR:TREATMENT_SUMMARY             	targeting GOLPH3 expression
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	Samples were fortified with an Internal standard Mix and lipids were extracted
SP:SAMPLEPREP_SUMMARY            	twice with an extraction mix consisting of 85:15 Ethyl acetate 70% Isopropanol.
SP:SAMPLEPREP_SUMMARY            	All lipids that were used in the Internal standard mix and in the Calibration
SP:SAMPLEPREP_SUMMARY            	mixes were purchased from Avanti Polar Lipids Inc. After evaporating the cell
SP:SAMPLEPREP_SUMMARY            	extract to dryness, the samples were reconstituted in the mobile phase.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Samples were analyzed with a Quantum Ultra triple quadrupole mass spectrometer
CH:CHROMATOGRAPHY_SUMMARY        	connected to an Accela HPLC and Accela autosampler using a solvent gradient.
CH:CHROMATOGRAPHY_SUMMARY        	Ceramides identity was achieved through MRM analysis with soft fragmentation.
CH:CHROMATOGRAPHY_SUMMARY        	Quantitative analysis is based on calibration curves generated for each
CH:CHROMATOGRAPHY_SUMMARY        	ceramide.
CH:INSTRUMENT_NAME               	Thermo Accela 1250
CH:COLUMN_NAME                   	Thermo Accucore C18 (100 2.1mm, 2.6um)
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
#MS
MS:INSTRUMENT_NAME               	Thermo Quantum Ultra
MS:INSTRUMENT_TYPE               	Triple quadrupole
MS:MS_TYPE                       	ESI
MS:MS_COMMENTS                   	Samples were analyzed with a Quantum Ultra triple quadrupole mass spectrometer
MS:MS_COMMENTS                   	connected to an Accela HPLC and Accela autosampler using a solvent gradient.
MS:MS_COMMENTS                   	Ceramides identity was achieved through MRM analysis with soft fragmentation.
MS:MS_COMMENTS                   	Quantitative analysis is based on calibration curves generated for each
MS:MS_COMMENTS                   	ceramide. J. Bielawski et al. / Methods 39 (2006) 82–91
MS:ION_MODE                      	POSITIVE
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS         	pmol
MS_METABOLITE_DATA_START
Samples	GOLPH3_OE_1	GOLPH3_OE_2	GOLPH3_OE_3	GOLPH3_KD_1	GOLPH3_KD_2	GOLPH3_KD_3	CTRL_1	CTRL_2	CTRL_3
Factors	Treatment:GOLPH3 overexpression	Treatment:GOLPH3 overexpression	Treatment:GOLPH3 overexpression	Treatment:GOLPH3 silencing	Treatment:GOLPH3 silencing	Treatment:GOLPH3 silencing	Treatment:no treatment	Treatment:no treatment	Treatment:no treatment	
C14_cer	4.4310	4.9560	3.8750	10.3440	9.9170	7.9090	9.4780	7.2560	5.9580
C14HexosylCer	1.0160	1.0110	1.0160	1.1430	1.3490	1.1270	1.2660	1.4170	1.3670
C14Lact-Cer									
C14-SM	71.7190	83.6620	64.7760	83.5500	89.0080	69.2890	118.1170	74.0240	67.6300
C16_cer	64.4760	72.6400	60.5150	180.7270	164.0680	134.8980	137.8050	112.3070	97.0640
C16HexosylCer	37.0560	39.4970	32.2980	57.3640	67.0940	46.5620	45.2060	61.3050	51.1870
C16Lact-Cer	26.9720	30.5260	26.1470	17.6030	19.9750	14.7640	28.3920	21.2350	19.1640
C16-SM	1678.8530	1864.6400	1532.4070	2002.1030	2118.5160	1656.6080	2692.3540	1543.9480	1445.6090
C18_1_cer	1.5210	1.6770	1.4370	3.0860	3.0170	2.4790	3.6530	2.8670	2.3390
C18_1HexosylCer	1.9130	1.8410	1.9230	2.1860	2.2760	2.0220	1.9910	1.9760	1.8830
C18_1Lact-Cer									
C18_1-SM	13.8440	13.8690	12.6290	14.4420	14.9560	13.0330	16.2120	16.9890	15.2390
C18_cer	7.2380	7.9580	7.0460	16.9600	15.8220	13.2960	17.7870	14.9720	12.9000
C18HexosylCer	3.1340	3.1360	2.6380	4.0740	4.2490	3.5170	3.0450	3.2200	2.9390
C18Lact-Cer	1.7720	1.9400	1.8490	1.7040	1.1660	1.2480	2.7540	1.3030	1.0450
C18-SM	53.4620	56.6890	50.2280	56.2920	54.4170	49.7470	58.1290	49.5250	46.1770
C20_1_cer	0.6130	0.6900	0.5920	1.1720	1.2750	0.9890	1.4110	1.1290	1.0540
C20_1HexosylCer	1.1930	1.1690	1.1590	1.3330	1.2180	1.2340	1.1860	1.2080	1.1670
C20_1Lact-Cer									
C20_1-SM	0.9220	0.6390	1.1230	1.3750	1.3820	1.5820	1.6030	0.8560	0.9580
C20_cer	2.6190	3.2090	2.6510	6.3300	5.7660	4.6020	7.2870	5.4150	4.8920
C20HexosylCer	1.0790	1.1770	1.0730	1.8260	2.0720	1.8530	1.1170	1.1520	1.0220
C20Lact-Cer								0.0780	
C20-SM				0.0190	0.4570				
C22_1_cer	5.9090	6.4380	5.3900	13.1980	12.8230	9.9100	14.8830	10.4820	9.7910
C22_1HexosylCer	2.2120	2.0980	2.0540	3.0120	3.3390	2.7880	2.3800	2.3160	2.3130
C22_1Lact-Cer	2.5120	2.3220	2.4040	2.3770	2.3870	2.7350	2.4300	2.3660	2.3320
C22_1-SM	56.8050	57.6410	53.4550	66.2790	67.5150	63.2760	71.6030	56.7040	54.6060
C22_cer	24.1280	27.7710	22.2760	55.3340	52.5650	39.1570	52.6490	35.8310	29.2280
C22HexosylCer	28.8450	31.4190	27.5880	62.3120	69.6760	52.0950	36.2100	32.6930	26.6760
C22Lact-Cer	15.3550	15.5060	15.7010	14.7750	15.4480	14.1230	14.6640	10.9620	9.3930
C22-SM	121.7610	127.9640	115.7780	162.8480	164.5950	155.2660	141.6070	113.4730	109.2640
C24_1_cer	48.4450	54.0400	44.1550	92.5140	88.5990	72.1990	87.5460	58.1060	53.4280
C24_1HexosylCer	46.8510	52.4380	43.9680	69.9880	82.5280	60.7520	51.7390	59.8930	48.1400
C24_1Lact-Cer	27.7180	31.2750	28.8860	23.5570	25.6330	21.0600	25.0900	20.5320	19.9680
C24_1-SM	469.0460	502.5510	457.1470	469.1120	527.5500	492.0790	503.4530	457.7070	449.1740
C24_cer	54.0040	62.1790	50.3500	84.2340	81.1030	63.3790	78.0290	38.9240	37.5670
C24HexosylCer	184.4370	186.9950	162.5500	303.9520	346.5530	263.4370	201.1330	177.1570	141.8690
C24Lact-Cer	67.0260	71.9230	63.6910	46.5980	51.6840	42.0480	53.8110	39.3110	33.4020
C24-SM	243.4400	263.7080	234.2220	304.6830	315.5030	293.8120	266.8470	251.2550	227.0420
C26_1_cer	3.3280	3.7210	3.1070	4.7360	5.1590	3.8990	4.8460	2.7230	2.6490
C26_1HexosylCer	9.4800	10.0550	8.6560	16.2270	18.6920	15.3400	10.9730	12.5400	10.8770
C26_1Lact-Cer	5.2910	5.4900	5.7320	4.9600	5.3040	4.5700	4.9030	4.5110	3.6600
C26_1-SM	13.6220	16.4840	13.3870	20.9100	23.5700	23.9730	18.4310	17.7830	15.8190
C26_cer	2.4540	2.5220	2.2000	2.5270	2.7690	2.2870	2.7110	1.5620	1.8110
C26HexosylCer	4.3910	5.0970	4.8240	6.9350	7.8200	6.3900	5.2010	3.7710	3.8670
C26Lact-Cer	2.2240	2.5880	2.2510	1.9820	2.3350	2.0430	2.0720	2.0090	1.8020
C26-SM	4.6180	4.3750	3.6500	6.1720	6.1450	5.4830	4.7180	4.3920	3.7730
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	pubchem_id	inchi_key	kegg_id	other_id	other_id_type	ri	ri_type	moverz_quant	
C14_cer						15.053			
C14HexosylCer						15.979			
C14Lact-Cer						15.552			
C14-SM						17.662			
C16_cer						16.57993424			
C16HexosylCer						17.160			
C16Lact-Cer						16.742			
C16-SM						18.481			
C18_1_cer						17.0608333			
C18_1HexosylCer						17.550			
C18_1Lact-Cer						16.744			
C18_1-SM						19.081			
C18_cer						17.93720568			
C18HexosylCer						18.167			
C18Lact-Cer						17.804			
C18-SM						19.711			
C20_1_cer						18.62231951			
C20_1HexosylCer						18.170			
C20_1Lact-Cer						17.808			
C20_1-SM						19.964			
C20_cer						19.3108956			
C20HexosylCer						19.233			
C20Lact-Cer						18.814			
C20-SM						20.845			
C22_1_cer						19.94082869			
C22_1HexosylCer						19.455			
C22_1Lact-Cer						19.037			
C22_1-SM						20.658			
C22_cer						20.77011827			
C22HexosylCer						20.404			
C22Lact-Cer						19.875			
C22-SM						21.602			
C24_1_cer						20.97331072			
C24_1HexosylCer						20.576			
C24_1Lact-Cer						20.046			
C24_1-SM						21.729			
C24_cer						22.3756384			
C24HexosylCer						22.562			
C24Lact-Cer						21.866			
C24-SM						22.988			
C26_1_cer						22.87423635			
C26_1HexosylCer						21.748			
C26_1Lact-Cer						21.109			
C26_1-SM						23.083			
C26_cer						24.53351824			
C26HexosylCer						23.258			
C26Lact-Cer						22.561			
C26-SM						24.624			
METABOLITES_END
#END