#METABOLOMICS WORKBENCH makita_20250522_061408 DATATRACK_ID:5936 STUDY_ID:ST003958 ANALYSIS_ID:AN006506 PROJECT_ID:PR002481
VERSION             	1
CREATED_ON             	June 10, 2025, 1:24 pm
#PROJECT
PR:PROJECT_TITLE                 	Comprehensive lipidomic analysis of six Hevea species and varieties related to
PR:PROJECT_TITLE                 	latex biosynthesis
PR:PROJECT_SUMMARY               	In this study, we performed lipidomic profiling of latex from Hevea brasiliensis
PR:PROJECT_SUMMARY               	RRIM600 and five Hevea species or varieties of similar age: H. guianensis, H.
PR:PROJECT_SUMMARY               	pauciflora, H. spruceana, H. collina, and H. confusa. Latex samples were
PR:PROJECT_SUMMARY               	analysed by LC-MS/MS, identifying 53 lipid molecules from five major categories
PR:PROJECT_SUMMARY               	and 16 classes. Among these, triacylglycerols (TG), phosphatidic acids (PA), and
PR:PROJECT_SUMMARY               	acylhexosyl sitosterols are major components. Comparative analysis revealed
PR:PROJECT_SUMMARY               	species-specific lipid profiles: H. guianensis and H. confusa exhibited high PA
PR:PROJECT_SUMMARY               	levels comparable to H. brasiliensis, whereas H. pauciflora, H. spruceana, and
PR:PROJECT_SUMMARY               	H. collina showed elevated TG and reduced PA content. Supervised OPLS-DA
PR:PROJECT_SUMMARY               	analysis separated H. brasiliensis from the other species and identified 18
PR:PROJECT_SUMMARY               	differentially abundant lipid molecules, including increased diacylglycerols and
PR:PROJECT_SUMMARY               	phosphatidic acids, and decreased hexosylceramides. These patterns may reflect
PR:PROJECT_SUMMARY               	underlying metabolic divergence with potential implications for latex
PR:PROJECT_SUMMARY               	composition and rubber biosynthesis. The dataset provides new insights into
PR:PROJECT_SUMMARY               	interspecific lipidome variation in Hevea and offers a valuable resource for
PR:PROJECT_SUMMARY               	future studies on lipid function in latex physiology and rubber properties.
PR:INSTITUTE                     	Maebashi Institute of Technology
PR:DEPARTMENT                    	Faculty of Engineering
PR:LABORATORY                    	Laboratory of Omics Science
PR:LAST_NAME                     	Makita
PR:FIRST_NAME                    	Yuko
PR:ADDRESS                       	460-1 Kamisadori-cho, Maebashi, Gunma, 371-0816, Japan
PR:EMAIL                         	makita@maebashi-it.ac.jp
PR:PHONE                         	+81-27-265-7366
PR:CONTRIBUTORS                  	Nyok-Sean Lau, miko Okubo-Kurihara, Minami Matsui
#STUDY
ST:STUDY_TITLE                   	Comprehensive lipidomic analysis of six Hevea species and varieties related to
ST:STUDY_TITLE                   	latex biosynthesis
ST:STUDY_SUMMARY                 	Latex, the raw material of natural rubber, is harvested from Hevea brasiliensis.
ST:STUDY_SUMMARY                 	Although there are related species within the Hevea genus, their latex is not
ST:STUDY_SUMMARY                 	suitable for product use due to its physicochemical properties. In this
ST:STUDY_SUMMARY                 	analysis, we focused on lipidomics to perform a comparative analysis aimed at
ST:STUDY_SUMMARY                 	identifying some of the factors underlying these differences.
ST:INSTITUTE                     	Maebashi Institute of Technology
ST:LAST_NAME                     	Yuko
ST:FIRST_NAME                    	Makita
ST:ADDRESS                       	460-1 Kamisadori-cho, Maebashi, Gunma 371-0816 Japan
ST:EMAIL                         	makita@maebashi-it.ac.jp
ST:PHONE                         	+81-27-265-7366
#SUBJECT
SU:SUBJECT_TYPE                  	Plant
SU:SUBJECT_SPECIES               	Hevea
SU:TAXONOMY_ID                   	3980 (genus Hevea)
SU:SPECIES_GROUP                 	Taxonomy_id (species): 1318718 (Hevea spruceana), 3981 (Hevea brasiliensis and
SU:SPECIES_GROUP                 	Hevea brasiliensis strain:RRIM 600), 882917 (Hevea guianensis var. guianensis),
SU:SPECIES_GROUP                 	882917 (Hevea guianensis var. collina), 1318717 (Hevea pauciflora), 1318717
SU:SPECIES_GROUP                 	(Hevea confusa is a synonym of Hevea pauciflora var. coriacea)
#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           	-	01_Hspruceana1	Sample source:Latex | Species:H. spruceana	RAW_FILE_NAME(Raw file name)=01_Hspruceana1_n.raw,01_Hspruceana1_p.raw
SUBJECT_SAMPLE_FACTORS           	-	02_Hspruceana2	Sample source:Latex | Species:H. spruceana	RAW_FILE_NAME(Raw file name)=02_Hspruceana2_n.raw,02_Hspruceana2_p.raw
SUBJECT_SAMPLE_FACTORS           	-	03_Hspruceana3	Sample source:Latex | Species:H. spruceana	RAW_FILE_NAME(Raw file name)=03_Hspruceana3_n.raw,03_Hspruceana3_p.raw
SUBJECT_SAMPLE_FACTORS           	-	04_Hconfusa1	Sample source:Latex | Species:H. confusa	RAW_FILE_NAME(Raw file name)=04_Hconfusa1_n.raw,04_Hconfusa1_p.raw
SUBJECT_SAMPLE_FACTORS           	-	05_Hconfusa2	Sample source:Latex | Species:H. confusa	RAW_FILE_NAME(Raw file name)=05_Hconfusa2_n.raw,05_Hconfusa2_p.raw
SUBJECT_SAMPLE_FACTORS           	-	06_Hconfusa3	Sample source:Latex | Species:H. confusa	RAW_FILE_NAME(Raw file name)=06_Hconfusa3_n.raw,06_Hconfusa3_p.raw
SUBJECT_SAMPLE_FACTORS           	-	07_Hcollina1	Sample source:Latex | Species:H. collina	RAW_FILE_NAME(Raw file name)=07_Hcollina1_n.raw,07_Hcollina1_p.raw
SUBJECT_SAMPLE_FACTORS           	-	08_Hcollina1	Sample source:Latex | Species:H. collina	RAW_FILE_NAME(Raw file name)=08_Hcollina1_n.raw,08_Hcollina1_p.raw
SUBJECT_SAMPLE_FACTORS           	-	09_Hcollina1	Sample source:Latex | Species:H. collina	RAW_FILE_NAME(Raw file name)=09_Hcollina1_n.raw,09_Hcollina1_p.raw
SUBJECT_SAMPLE_FACTORS           	-	10_RRIM600R1	Sample source:Latex | Species:H. brasiliensis RRIM 600	RAW_FILE_NAME(Raw file name)=10_RRIM600R1_n.raw,10_RRIM600R1_p.raw
SUBJECT_SAMPLE_FACTORS           	-	11_RRIM600R2	Sample source:Latex | Species:H. brasiliensis RRIM 600	RAW_FILE_NAME(Raw file name)=11_RRIM600R2_n.raw,11_RRIM600R2_p.raw
SUBJECT_SAMPLE_FACTORS           	-	12_RRIM600R3	Sample source:Latex | Species:H. brasiliensis RRIM 600	RAW_FILE_NAME(Raw file name)=12_RRIM600R3_n.raw,12_RRIM600R3_p.raw
SUBJECT_SAMPLE_FACTORS           	-	13_HguianensisR1	Sample source:Latex | Species:H. guianensis	RAW_FILE_NAME(Raw file name)=13_HguianesisR1_n.raw,13_HguianesisR1_p.raw
SUBJECT_SAMPLE_FACTORS           	-	14_HguianensisR2	Sample source:Latex | Species:H. guianensis	RAW_FILE_NAME(Raw file name)=14_HguianesisR2_n.raw,14_HguianesisR2_p.raw
SUBJECT_SAMPLE_FACTORS           	-	15_HguianensisR3	Sample source:Latex | Species:H. guianensis	RAW_FILE_NAME(Raw file name)=15_HguianesisR3_n.raw,15_HguianesisR3_p.raw
SUBJECT_SAMPLE_FACTORS           	-	19_Hpauciflora1	Sample source:Latex | Species:H. pauciflora	RAW_FILE_NAME(Raw file name)=19_Hpauciflora1_n.raw,19_Hpauciflora1_p.raw
SUBJECT_SAMPLE_FACTORS           	-	20_Hpauciflora2	Sample source:Latex | Species:H. pauciflora	RAW_FILE_NAME(Raw file name)=20_Hpauciflora2_n.raw,20_Hpauciflora2_p.raw
SUBJECT_SAMPLE_FACTORS           	-	21_Hpauciflora3	Sample source:Latex | Species:H. pauciflora	RAW_FILE_NAME(Raw file name)=21_Hpauciflora3_n.raw,21_Hpauciflora3_p.raw
#COLLECTION
CO:COLLECTION_SUMMARY            	All samples used in this study were obtained from mature, seven-year-old H.
CO:COLLECTION_SUMMARY            	brasiliensis and other Hevea species grown at the same location within the
CO:COLLECTION_SUMMARY            	plantation of the Rubber Research Institute of Indonesia. Latex samples were
CO:COLLECTION_SUMMARY            	harvested for lipidomic analyses. To standardize latex sampling, each tree was
CO:COLLECTION_SUMMARY            	tapped once on the same morning, and 2 mL of latex was collected immediately
CO:COLLECTION_SUMMARY            	after tapping. The trees are maintained as a species collection for research
CO:COLLECTION_SUMMARY            	purposes; they were not part of a commercial plantation and thus were not
CO:COLLECTION_SUMMARY            	regularly tapped.
CO:SAMPLE_TYPE                   	Latex
CO:COLLECTION_METHOD             	Tapping
CO:COLLECTION_LOCATION           	Sembawa, Indonesia
#TREATMENT
TR:TREATMENT_SUMMARY             	No special treatment was applied other than sample preparation.
TR:PLANT_GROWTH_SUPPORT          	seven-year-old
TR:PLANT_GROWTH_LOCATION         	Sembawa, Indonesia
#SAMPLEPREP
SP:SAMPLEPREP_SUMMARY            	100 µL of chloroform was added to 1 mg of latex samples, followed by shaking,
SP:SAMPLEPREP_SUMMARY            	sonication, and centrifugation. Methanol was then added to 50 µL of the
SP:SAMPLEPREP_SUMMARY            	supernatant, stirred, and centrifuged again, and the supernatant was collected.
SP:SAMPLEPREP_SUMMARY            	Lysophosphatidylcholine (18:1-d7) was added as an internal standard at a final
SP:SAMPLEPREP_SUMMARY            	concentration of 500 ng/mL, and the sample was analysed using LC-MS/MS.
#CHROMATOGRAPHY
CH:CHROMATOGRAPHY_SUMMARY        	Chromatographic separation was achieved using an L-column3 C18 metal-free column
CH:CHROMATOGRAPHY_SUMMARY        	(2.0 mm I.D. × 100 mm, 2 µm particle size; CERI). Solvent A: 59% ultrapure
CH:CHROMATOGRAPHY_SUMMARY        	water; 40% acetonitrile; 1% 1 M ammonium formate solution; 0.1% formic acid.
CH:CHROMATOGRAPHY_SUMMARY        	Solvent B: 90% 2-propanol; 9% acetonitrile; 1% 1 M ammonium formate
CH:CHROMATOGRAPHY_SUMMARY        	solution;0.1% formic acid.
CH:CHROMATOGRAPHY_TYPE           	Reversed phase
CH:INSTRUMENT_NAME               	Thermo Dionex Ultimate 3000 RS
CH:COLUMN_NAME                   	CERI L-column3 C18 Metal-Free column (100 x 2mm, 2µm)
CH:SOLVENT_A                     	60% water/40% acetonitrile; 10 mM ammonium formate solution; 0.1% formic acid
CH:SOLVENT_B                     	90% Isopropanol/10% acetonitrile; 10mM ammonium formate;0.1% formic acid
CH:FLOW_GRADIENT                 	Time (min):%B: 0.0:25, 0.5:25, 6.5:60, 21.5:90, 22.0:99, 26.0:99, 26.1:25,
CH:FLOW_GRADIENT                 	35.0:25
CH:FLOW_RATE                     	0.2 mL/min
CH:COLUMN_TEMPERATURE            	55℃
#ANALYSIS
AN:ANALYSIS_TYPE                 	MS
AN:SOFTWARE_VERSION              	MS-DIAL Ver.4.80
#MS
MS:INSTRUMENT_NAME               	Thermo LTQ XL
MS:INSTRUMENT_TYPE               	Orbitrap
MS:MS_TYPE                       	ESI
MS:ION_MODE                      	NEGATIVE
MS:MS_COMMENTS                   	-
#MS_METABOLITE_DATA
MS_METABOLITE_DATA:UNITS	peak area
MS_METABOLITE_DATA_START
Samples	01_Hspruceana1	02_Hspruceana2	03_Hspruceana3	04_Hconfusa1	05_Hconfusa2	06_Hconfusa3	07_Hcollina1	08_Hcollina1	09_Hcollina1	10_RRIM600R1	11_RRIM600R2	12_RRIM600R3	13_HguianensisR1	14_HguianensisR2	15_HguianensisR3	19_Hpauciflora1	20_Hpauciflora2	21_Hpauciflora3
Factors	Sample source:Latex | Species:H. spruceana	Sample source:Latex | Species:H. spruceana	Sample source:Latex | Species:H. spruceana	Sample source:Latex | Species:H. confusa	Sample source:Latex | Species:H. confusa	Sample source:Latex | Species:H. confusa	Sample source:Latex | Species:H. collina	Sample source:Latex | Species:H. collina	Sample source:Latex | Species:H. collina	Sample source:Latex | Species:H. brasiliensis RRIM 600	Sample source:Latex | Species:H. brasiliensis RRIM 600	Sample source:Latex | Species:H. brasiliensis RRIM 600	Sample source:Latex | Species:H. guianensis	Sample source:Latex | Species:H. guianensis	Sample source:Latex | Species:H. guianensis	Sample source:Latex | Species:H. pauciflora	Sample source:Latex | Species:H. pauciflora	Sample source:Latex | Species:H. pauciflora
ADGGA 18:2_18:2_18:2	450147	623060	916408	369096	864919	1227046	30725	15426	158655	283516	218887	541204	172320	70645	60971	84014	44091	1025565
CL 12:0_16:0_18:2_18:2	970522	1122186	202666	3609248	844866	3141541	675719	763888	483855	1250933	633915	2767653	827945	233749	305258	2360484	0	608045
LPC 18:1(d7)	8214966	8999635	9433805	8108387	8783637	8287926	8325622	9349171	8320511	7796616	8958212	8708741	8427152	9549026	8314638	9123133	8974850	7839076
FA 24:0;(2OH)	778903	433437	1309009	468935	1212401	62185	308880	949258	773706	481768	488363	357243	743605	667258	369773	210828	465813	804390
PA 16:0_18:1	531697	361430	97242	1809647	557812	3528027	353854	285793	225649	1192990	637702	2355824	352948	142765	111929	1920520	43326	313075
PA 18:0_18:1	2594256	1412998	490594	4767462	5030516	16252028	862762	262608	1216488	5200540	3444846	7965898	417239	498798	390354	3056137	39804	1144899
PA 18:1_18:1	5744604	4642701	1602118	11034520	5775558	20456470	2293380	1087310	2762875	8755839	5759336	14384474	2005037	1494466	1511410	7401013	218977	2462494
PA 18:1_18:2	5309347	4968588	1020837	9622447	1961710	11715318	1923078	966394	2023202	6201100	4041049	12385438	1523810	1364982	1510524	6345974	77455	1691863
PA 18:2_18:2	3485571	4274661	704119	6110754	3825567	4782886	1045805	458280	1090776	2331366	1541519	6139068	952752	636213	824287	2755021	23690	1102377
PI 16:0_18:2	4650805	237511	707240	1902765	598873	357057	183808	179053	1352139	388252	167329	113258	101869	239173	160663	1733357	44818	178407
MS_METABOLITE_DATA_END
#METABOLITES
METABOLITES_START
metabolite_name	Adduct type	Reference m/z	Formula	Ontology	Rt(min)	Average Mz
ADGGA 18:2_18:2_18:2	[M-H]-	1053.76123	C63H106O12	ADGGA	23.2	1053.75916
CL 12:0_16:0_18:2_18:2	[M-2H]2-	671.44751	C73H134O17P2	CL	17.7	671.46484
LPC 18:1(d7)	[M+HCOO]-	573.39026	C26H45D7NO7P	LPC	9.2	573.38892
FA 24:0;(2OH)	[M-H]-	383.35309	C24H48O3	OxFA	17	383.35303
PA 16:0_18:1	[M-H]-	673.48138	C37H71O8P	PA	18.7	673.48157
PA 18:0_18:1	[M-H]-	701.5127	C39H75O8P	PA	19.9	701.50793
PA 18:1_18:1	[M-H]-	699.49701	C39H73O8P	PA	19	699.49695
PA 18:1_18:2	[M-H]-	697.48138	C39H71O8P	PA	17.9	697.48071
PA 18:2_18:2	[M-H]-	695.4657	C39H69O8P	PA	16.9	695.46625
PI 16:0_18:2	[M-H]-	833.51862	C43H79O13P	PI	16.7	833.51855
METABOLITES_END
#END