Cannabis sativa Species Overview

Experiment: MedPlntConsort (Medicinal Plant Consortium - metabolomic and transcriptomic data from selected plant materials)

Co-analysis of metabolomics and transcriptomics data is available. To identify the transcripts whose levels are most closely correlated with a metabolite, click on that metabolite. In the window that opens, click on [Go to omics analysis]

Sample Name	Replicates	Description
Buds	5
Flowers	5
Mature Leaves	4
Roots	5
Shoots	4
Young Leaves	4

1 Platforms

Platform: Cannabis LC/TOF MS Negative Ion

View Data Download Data Raw Data

+ LC-TOF metadata
+ MarkerLynx metadata
+ QuanLynx metadata

+ Biological metadata

Metabolite Search

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Chemically defined metabolites in this experiment:

Cannabichromene
        MDC-CAN-HPLC-E-NEG-F1-313.216-17.39 [M-H]-
Cannabidiol
        MDC-CAN-HPLC-E-NEG-F1-313.213-14.7 [M-H]-
Cannabidiolic acid
        MDC-CAN-HPLC-E-NEG-F1-1111.567-14.56 [3M+K-2H]-
Cannabidiolic acid
        MDC-CAN-HPLC-E-NEG-F1-357.205-14.57 [M-H]-
Cannabidiolic acid
        MDC-CAN-HPLC-E-NEG-F1-737.393-14.57 [2M+Na-2H]-
Cannabigerol
        MDC-CAN-HPLC-E-NEG-F1-315.232-14.76 [M-H]-
Cannabigerol
        MDC-CAN-HPLC-E-NEG-F1-631.467-14.72 [2M-H]-
Cannabigerolic acid
        MDC-CAN-HPLC-E-NEG-F1-1117.612-14.92 [3M+K-2H]-
Cannabigerolic acid
        MDC-CAN-HPLC-E-NEG-F1-359.222-14.95 [M-H]-
Cannabigerolic acid
        MDC-CAN-HPLC-E-NEG-F1-741.427-14.94 [2M+Na-2H]-
Cannabinol
        MDC-CAN-HPLC-E-NEG-F1-309.183-15.9 [M-H]-
Cannabinolic acid
        MDC-CAN-HPLC-E-NEG-F1-1083.493-16.02 [3M+Na-2H]-
Cannabinolic acid
        MDC-CAN-HPLC-E-NEG-F1-1099.471-16 [3M+K-2H]-
Cannabinolic acid
        MDC-CAN-HPLC-E-NEG-F1-353.175-16.04 [M-H]-
Cannabinolic acid
        MDC-CAN-HPLC-E-NEG-F1-729.332-16.01 [2M+Na-2H]-
Cannabispiranol
        MDC-CAN-HPLC-E-NEG-F1-247.131-9.53 [M-H]-
Cannabistilbene isomer 1
        MDC-CAN-HPLC-E-NEG-F1-303.121-7.6 [M-H]-
Cannabistilbene isomer 2
        MDC-CAN-HPLC-E-NEG-F1-303.12-8.02 [M-H]-
Cannflavin A or Cannflavin C
        MDC-CAN-HPLC-E-NEG-F1-435.175-14.18 [M-H]-
Cannflavin A or Cannflavin C
        MDC-CAN-HPLC-E-NEG-F1-435.178-15.44 [M-H]-
Cannflavin B
        MDC-CAN-HPLC-E-NEG-F1-367.116-12.53 [M-H]-
Cannflavin B
        MDC-CAN-HPLC-E-NEG-F1-735.238-12.5 [2M-H]-
Delta-9-tetrahydrocannabinol
        MDC-CAN-HPLC-E-NEG-F1-313.215-16.48 [M-H]-
Delta-9-tetrahydrocannabinol
        MDC-CAN-HPLC-E-NEG-F1-627.438-16.48 [2M-H]-
Delta-9-tetrahydrocannabinolic acid
        MDC-CAN-HPLC-E-NEG-F1-1095.593-17.23 [3M+Na-2H]-
Delta-9-tetrahydrocannabinolic acid
        MDC-CAN-HPLC-E-NEG-F1-1111.568-17.24 [3M+K-2H]-
Delta-9-tetrahydrocannabinolic acid
        MDC-CAN-HPLC-E-NEG-F1-1491.747-17.22 [4M+Na+K-3H]-
Delta-9-tetrahydrocannabinolic acid
        MDC-CAN-HPLC-E-NEG-F1-357.2-17.25 [M-H]-
Delta-9-tetrahydrocannabinolic acid
        MDC-CAN-HPLC-E-NEG-F1-737.398-17.27 [2M+Na-2H]-
Orientin
        MDC-CAN-HPLC-E-NEG-F1-447.091-3.82 [M-H]-
Orientin
        MDC-CAN-HPLC-E-NEG-F1-895.188-3.84 [2M-H]-
Orientin hexoside or Flavocannabiside
        MDC-CAN-HPLC-E-NEG-F1-1219.283-3.89 [2M-H]-
Orientin hexoside or Flavocannabiside
        MDC-CAN-HPLC-E-NEG-F1-609.141-3.91 [M-H]-
Orientin rhamnoside (3.1 min); Vitexin hexoside (4.1 min)
        MDC-CAN-HPLC-E-NEG-F1-1187.292-3.93 [2M-H]-
Orientin rhamnoside (3.1 min); Vitexin hexoside (4.1 min)
        MDC-CAN-HPLC-E-NEG-F1-593.147-3.93 [M-H]-
Propyl-4-hydroxybenzoate standard
        MDC-CAN-HPLC-E-NEG-F1-136.016-7.33
Propyl-4-hydroxybenzoate standard
        MDC-CAN-HPLC-E-NEG-F1-137.024-7.34 fragment
Propyl-4-hydroxybenzoate standard
        MDC-CAN-HPLC-E-NEG-F1-179.071-7.33 [M-H]-
Quercetin dihexoside
        MDC-CAN-HPLC-E-NEG-F1-625.136-3.75 [M-H]-
sucrose
        MDC-CAN-HPLC-E-NEG-F1-341.109-0.49 [M-H]-
sucrose
        MDC-CAN-HPLC-E-NEG-F1-377.087-0.46 [M+Cl]-
sucrose
        MDC-CAN-HPLC-E-NEG-F1-683.224-0.49 [2M-H]-
Telmisartan standard
        MDC-CAN-HPLC-E-NEG-F1-513.229-12.12 [M-H]-
Tetrahydrocannabinolic acid - C4
        MDC-CAN-HPLC-E-NEG-F1-343.19-16.41 [M-H]-
Tetrahydrocannabiorcolic acid isomer I
        MDC-CAN-HPLC-E-NEG-F1-301.144-13.76 [M-H]-
Tetrahydrocannabiorcolic acid isomer I
        MDC-CAN-HPLC-E-NEG-F1-625.271-13.74 [2M+Na-2H]-
Tetrahydrocannabiorcolic acid isomer I
        MDC-CAN-HPLC-E-NEG-F1-943.382-13.72 [3M+K-2H]-
Tetrahydrocannabiorcolic acid isomer II
        MDC-CAN-HPLC-E-NEG-F1-301.14-14.24 [M-H]-
Tetrahydrocannabivarin
        MDC-CAN-HPLC-E-NEG-F1-285.183-14.58 [M-H]-
Vitexin
        MDC-CAN-HPLC-E-NEG-F1-431.097-4.04 [M-H]-
Vitexin
        MDC-CAN-HPLC-E-NEG-F1-863.198-4.03 [2M-H]-
Vitexin rhamnoside
        MDC-CAN-HPLC-E-NEG-F1-1155.299-4.14 [2M-H]-
Vitexin rhamnoside
        MDC-CAN-HPLC-E-NEG-F1-577.152-4.14 [M-H]-

Volcano Plot?

Protocol for LC-TOF
LabPI	A. Daniel Jones
Analyst	Mary Dawn Celiz
LC system	Prominence High Performace Liquid Chromatograph
Manufacturer	Shimadzu
Degasser	DGU-20A5
Solvent Delivery	LC-20AD
System Controller	SCL-10AVP
Autosampler	SIL-50000
Column Oven	CTO-20A
Column	Ascentis
Manufacturer of column	Supelco
Catalogue number	53822-U
Serial number	USMD003586
Packing Lot number	S10035
Injection volume	10 uL
Flow rate	0.3 mL/min
Mobile phases
A	0.5 mM ammonium acetate, pH 3.85
B	MeOH
Gradient Profile	Gradient program started with 1% B- 99% A, held for one minute, increased to 30% B in 1.5 minutes, then increased to 50% B in 5.5 minutes, further increase to 70% B in four minutes, followed by 99% B in ten minutes, held at 99 % B for four minutes, decreased to 1% B in one minute, held at 1% B for three minutes resulting to a total run time of 30 minutes
Column oven temperature	50
Sample temperature in the autosampler	10
Inlet method name	NIH_CAN_OPT_AscExp_004
Mass Spectrometer	Micromass? LCT PremierTM time-of-flight (TOF) mass spectrometer
Manufacturer	Waters
Software	MassLynxTM Version 4.1
Ionization source	Electrospray ionization (ESI)
Data acquisition	W mode, centroid
Polarity	Positive and Negative
Mass Range	50-1500 m/z
Aperture 1 voltage
Function 1	20 V
Function 2	40 V
Function 3	60 V
Function 4	80 V
MS method file	MDC_CAN_pos or MDC_CAN_neg
Manipulation of data
Lock mass	Telmisartan was used as lock mass standard.

Protocol for MarkerLynx
Function	1
Initial Retention Time (min)	0.3
Final Retention Time (min)	21
Low Mass	50
High Mass	1500
Mass Tolerance (Da)	0.05
Apex Track Peak Parameters
Peak Width at 5% Height (seconds)	automatic
Peak-to-Peak Baseline Noise	automatic
Apply smoothing	Yes
Collection Parameters
Marker Intensity threshold (counts)	20
Mass Window (Da)	0.05
Retention Time Window (min)	0.2
Noise Elimintation Level	10
Deisotope Data	Yes

Protocol for QuanLynx
Use absolute mass window	Yes
Chromatogram Mass Window (Da)	0.05
Response Type	External (absolute)
Response Uses	Area
Concentration of Standard (?M)	0.25, 0.5, 1, 2.5, 5, 10, 20
Retention Time Parameters
Locate Peak Using	Retention time
Retention Time Window (min) ?	0.2
Locate Peak Selection	Largest
Calibration Properties
Polynomial Type	Linear
Calibration Origin	Force
Weighing Function	1/X
Concentration Units
Integration Properties
Smoothing Enabled	YES
Smooth Parameters
Smoothing Method	Mean
Smooting Iterations	1
Smoothing Width	2
Apex Track Enables	Yes
Apex Track Parameters
Peak-to-Peak Baseline Noise	Automatic
Peak width at 5% height	Automatic
Baseline Start Threshold %	0
Baseline End Threshold %	0.5

Data Source
Data from the Medicinal Plant Consortium (MPC), an NIH supported project (GM092521) focused on harnessing knowledge from medicinal plant species. Natural products from plants serve as rich resources for drug development with almost 100 plant-derived compounds in clinical trials in 2007. Plant derived natural products have had a profound and lasting impact on human health and include compounds successfully used for decades such as digitalis, vincristine, Taxol and morphine isolated from foxglove, periwinkle, yew, and opium poppy. The enormous structural diversity and biological activities of plant-derived compounds suggest that additional, medicinally relevant compounds remain to be discovered in plants. MPC [metabolomics; transcriptomics data] encompasses 13 collaborating research units from 7 institutions.
Publications
Crispin MC, Wurtele ES. 2012. Use of Metabolomics and Transcriptomics to Gain Insights into the Regulation and Biosynthesis of Medicinal Compounds: Hypericum as a Model. Chapter 18 In:S Chandra, H Lata, AVarma, ed., Biotechnology for Medicinal Plants: Propagation and improvement. Springer. pp 395-411. Wurtele ES, ChappellJ, Jones AD, Celiz MD, Ransom N, Hur M, Rizshsky L, Dixon P Liu J, Widrlechner MP, Nikolau BJ. 2012. Medicinal Plants: A Public Resource for Metabolomics and Hypothesis Development. Metabolites. 2(4), 1031-1059; doi:10.3390/metabo2041031 Yeo YS, S. Nybo E, Chittiboyina AG, Weerasooriya AD, Wang YH, Góngora‐Castillo E, Vaillancourt B, Buell CR, DellaPenna D, Celiz MD, Jones AD, Wurtele ES, Ransom N, Dudareva N, Shabaan KA, Tibrewal N, Chandra S, Smillie T, Khan IA, Coates RM, Watt DS, Chappell J. 2012. Functional identification of valerena-1,10-diene synthase, a terpene synthase catalyzing a unique chemical cascade in the biosynthesis of biologically active sesquiterpenes in Valeriana officinalis. J Biol Chem. doi:10.1074