Camptotheca acuminata Species Overview

Experiment: MedPlntConsort (group 1) (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
Bark - Young	4
Leaf - Immature (25 75%)	3
Leaf - Mature (Fully Expanded)	3
Root - Entire Root	4

1 Platforms

Platform: Camptotheca acuminata - LC/TOF MS Positive Ion

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+ LC-TOF metadata
+ MarkerLynx metadata
+ QuanLynx metadata

+ Biological metadata

Metabolite Search

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Chemically defined metabolites in this experiment:

10-Hydroxycamptothecin
        MDC-Cam-HPLC-E-POS-F1-365.113-12.79 [M+H]+
10-Hydroxycamptothecin
        MDC-Cam-HPLC-E-POS-F1-751.215-12.77 [2M+Na]+
Camptothecin
        MDC-Cam-HPLC-E-POS-F1-1067.338-14.1 [3M+Na]+
Camptothecin
        MDC-Cam-HPLC-E-POS-F1-349.116-14.03 [M+H]+
Camptothecin
        MDC-Cam-HPLC-E-POS-F1-371.108-14.08 [M+Na]+
Camptothecin
        MDC-Cam-HPLC-E-POS-F1-697.232-14.08 [2M+H]+
Camptothecin
        MDC-Cam-HPLC-E-POS-F1-719.204-14.02 [2M+Na]+
Camptothecin
        MDC-Cam-HPLC-E-POS-F1-735.196-14.07 [2M+K]+
Chlorogenic acid, isomer 1
        MDC-Cam-HPLC-E-POS-F1-355.101-4.14 [M+H]+
Chlorogenic acid, isomer 1
        MDC-Cam-HPLC-E-POS-F1-372.139-4.14 [M+NH4]+
Chlorogenic acid, isomer 1
        MDC-Cam-HPLC-E-POS-F1-393.068-4.16 [M+K]+
Chlorogenic acid, isomer 1
        MDC-Cam-HPLC-E-POS-F1-726.241-4.16 [2M+NH4]+
Chlorogenic acid, isomer 1
        MDC-Cam-HPLC-E-POS-F1-731.195-4.12 [2M+Na]+
Chlorogenic acid, isomer 2
        MDC-Cam-HPLC-E-POS-F1-355.111-5.88 [M+H]+
Chlorogenic acid, isomer 2
        MDC-Cam-HPLC-E-POS-F1-372.138-5.87 [M+NH4]+
Ciprofloxacin
        MDC-Cam-HPLC-E-POS-F1-332.141-7 [M+H]+
Coumaroyl quinic acid
        MDC-Cam-HPLC-E-POS-F1-147.049-5.47 fragment
Coumaroyl quinic acid
        MDC-Cam-HPLC-E-POS-F1-339.111-5.5 [M+H]+
Coumaroyl quinic acid
        MDC-Cam-HPLC-E-POS-F1-361.1-5.48 [M+Na]+
Coumaroyl quinic acid
        MDC-Cam-HPLC-E-POS-F1-699.203-5.47 [2M+Na]+
Deoxypumiloside isomer 1
        MDC-Cam-HPLC-E-POS-F1-1015.355-14.85 [2M+Na]+
Deoxypumiloside isomer 1
        MDC-Cam-HPLC-E-POS-F1-497.187-14.86 [M+H]+
Deoxypumiloside isomer 1
        MDC-Cam-HPLC-E-POS-F1-993.37-14.86 [2M+H]+
Deoxypumiloside isomer 2
        MDC-Cam-HPLC-E-POS-F1-1015.344-15.67 [2M+Na]+
Deoxypumiloside isomer 2
        MDC-Cam-HPLC-E-POS-F1-497.188-15.68 [M+H]+
Deoxypumiloside isomer 2
        MDC-Cam-HPLC-E-POS-F1-993.365-15.67 [2M+H]+
Hydroxy (or epoxy) strictosidine
        MDC-Cam-HPLC-E-POS-F1-515.199-8.9 [M+H]+
Kaempferol hexoside, p-coumaroyl ester, isomer 1
        MDC-Cam-HPLC-E-POS-F1-1211.287-14.25 [2M+Na]+
Kaempferol hexoside, p-coumaroyl ester, isomer 1
        MDC-Cam-HPLC-E-POS-F1-595.157-14.26 [M+H]+
Kaempferol hexoside, p-coumaroyl ester, isomer 1
        MDC-Cam-HPLC-E-POS-F1-617.139-14.26 [M+Na]+
Kaempferol hexoside, p-coumaroyl ester, isomer 2
        MDC-Cam-HPLC-E-POS-F1-1211.275-14.86 [2M+Na]+
Kaempferol hexoside, p-coumaroyl ester, isomer 2
        MDC-Cam-HPLC-E-POS-F1-595.152-14.92 [M+H]+
Kaempferol hexoside, p-coumaroyl ester, isomer 2
        MDC-Cam-HPLC-E-POS-F1-617.131-14.87 [M+Na]+
Kaempferol-3-O-hexoside isomer 1
        MDC-Cam-HPLC-E-POS-F1-287.061-10.7 fragment
Kaempferol-3-O-hexoside isomer 1
        MDC-Cam-HPLC-E-POS-F1-449.112-10.71 [M+H]+
Kaempferol-3-O-hexoside isomer 2
        MDC-Cam-HPLC-E-POS-F1-287.061-11.36 fragment
Kaempferol-3-O-hexoside isomer 2
        MDC-Cam-HPLC-E-POS-F1-449.105-11.31 [M+H]+
Kaempferol-3-O-hexoside isomer 2
        MDC-Cam-HPLC-E-POS-F1-919.203-11.29 [2M+Na]+
Loganic acid
        MDC-Cam-HPLC-E-POS-F1-377.143-5.51 [M+H]+
Loganic acid
        MDC-Cam-HPLC-E-POS-F1-394.168-5.49 [M+NH4]+
Loganic acid
        MDC-Cam-HPLC-E-POS-F1-770.316-5.54 [2M+NH4]+
Loganic acid
        MDC-Cam-HPLC-E-POS-F1-775.281-5.61 [2M+Na]+
Methoxycamptothecin
        MDC-Cam-HPLC-E-POS-F1-379.135-15.22 [M+H]+
Methoxycamptothecin
        MDC-Cam-HPLC-E-POS-F1-779.242-15.22 [2M+Na]+
Pumiloside isomer 1
        MDC-Cam-HPLC-E-POS-F1-1025.365-12.29 [2M+H]+
Pumiloside isomer 1
        MDC-Cam-HPLC-E-POS-F1-513.183-12.3 [M+H]+
Pumiloside isomer 2
        MDC-Cam-HPLC-E-POS-F1-1025.377-13.4 [2M+H]+
Pumiloside isomer 2
        MDC-Cam-HPLC-E-POS-F1-1047.359-13.48 [2M+Na]+
Pumiloside isomer 2
        MDC-Cam-HPLC-E-POS-F1-513.185-13.46 [M+H]+
Quercetin-3-O-hexoside
        MDC-Cam-HPLC-E-POS-F1-303.057-9.92 fragment
Quercetin-3-O-hexoside
        MDC-Cam-HPLC-E-POS-F1-465.097-9.84 [M+H]+
Quercetin-3-O-hexoside
        MDC-Cam-HPLC-E-POS-F1-951.193-9.85 [2M+Na]+
Secologanic acid
        MDC-Cam-HPLC-E-POS-F1-375.128-6 [M+H]+
Stricosamide isomer 2
        MDC-Cam-HPLC-E-POS-F1-499.204-16.7 [M+H]+
Strictosamide diol
        MDC-Cam-HPLC-E-POS-F1-533.214-15.15 [M+H]+
Strictosamide isomer 1
        MDC-Cam-HPLC-E-POS-F1-1019.407-15.36 [2M+Na]+
Strictosamide isomer 1
        MDC-Cam-HPLC-E-POS-F1-499.21-15.38 [M+H]+
Strictosamide isomer 1
        MDC-Cam-HPLC-E-POS-F1-997.425-15.37 [2M+H]+
Strictosamide isomer 2
        MDC-Cam-HPLC-E-POS-F1-1019.405-16.7 [2M+Na]+
Strictosamide isomer 2
        MDC-Cam-HPLC-E-POS-F1-997.425-16.7 [2M+H]+
Strictosidinic acid isomer 1
        MDC-Cam-HPLC-E-POS-F1-1033.427-9.5 [2M+H]+
Strictosidinic acid isomer 1
        MDC-Cam-HPLC-E-POS-F1-517.215-9.51 [M+H]+
Strictosidinic acid isomer 2
        MDC-Cam-HPLC-E-POS-F1-1033.419-10.33 [2M+H]+
Strictosidinic acid isomer 2
        MDC-Cam-HPLC-E-POS-F1-517.212-10.38 [M+H]+
sucrose
        MDC-Cam-HPLC-E-POS-F1-365.111-0.46 [M+Na]+
sucrose
        MDC-Cam-HPLC-E-POS-F1-381.081-0.47 [M+K]+
Telmisartan
        MDC-Cam-HPLC-E-POS-F1-515.239-17.4 [M+H]+
Tryptamine
        MDC-Cam-HPLC-E-POS-F1-144.085-2.31 fragment
Tryptamine
        MDC-Cam-HPLC-E-POS-F1-161.112-2.31 [M+H]+
Vogeloside isomer 1
        MDC-Cam-HPLC-E-POS-F1-389.144-7.86 [M+H]+
Vogeloside isomer 1
        MDC-Cam-HPLC-E-POS-F1-411.137-7.82 [M+Na]+
Vogeloside isomer 1
        MDC-Cam-HPLC-E-POS-F1-427.109-7.83 [M+K]+
Vogeloside isomer 2
        MDC-Cam-HPLC-E-POS-F1-389.143-8.18 [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	USMD002915
Packing Lot number	S09038
Injection volume	10
Flow rate	0.3 mL/min
Mobile phases
A	10 mM NH4HCOO, pH 2.85
B	MeOH
Gradient Profile	Gradient program started with 1% B- 99% A, held for one minute, increased to 25% B in nine minutes, then 99% B in 14 minutes, held at 99 % B for three minutes, decreased to 1% B in one minute, held at 1% B for three minutes resulting to a total run time of 31 minutes
Column oven temperature	50
Sample temperature in the autosampler	10
Inlet method name	NIH_Campt_OPT_AscExp_002
Mass Spectrometer	Micromass
Manufacturer	Waters
Software	MassLynxTM Version 4.1
Ionization source	Electrospray ionization (ESI)
Data acquisition	W mode, centroid
Polarity	Positive and Negative
Mass Range	m/z 50-1500
Aperture 1 voltage
Function 1	20 V
Function 2	40 V
Function 3	60 V
Function 4	80 V
MS method file	MDC_OPT_pos or MDC_OPT_neg
Manipulation of data
Lock mass	Ciprofloxacin was used as lock mass standard.

Protocol for MarkerLynx
Function	1
Initial Retention Time (min)	0.35
Final Retention Time (min)	20
Low Mass	50
High Mass	1500
Mass Tolerance (Da)	0.05
Apex Track Peak Parameters
Peak Width at 5% Height (seconds)	25
Peak-to-Peak Baseline Noise	150
Collection Parameters
Masses per Retention Time	20
Minimum Intensity ( as a percentage of the ba	5
Mass Window (Da)	0.05
Retention Time Window (min)	0.35
Noise Elimintation Level	20
Deisotope Data	YES

Protocol for QuanLynx
Include Primary Trace in Response	YES
Use absolute mass window	YES
Chromatogram Mass Window (Da)	0.05
Response Type	External (absolute)
Response Uses	Area
Acquisition Function Number	1
Concentration of Standard (?M)	0.1, 0.5, 1, 2.5, 5, 10
Retention Time Parameters
Locate Peak Using	Retention Time
Retention Time Window (min) ?	0.5
Locate Peak Selection	Largest
Calibration Properties
Polynomial Type	Linear
Origin	Force
Weighing Function	1/X
Axis Transformation	None
Concentration Units
Integration Properties
Smoothing Enabled	YES
Smooth Parameters
Smoothing Method	Mean
Smooting Iterations	1
Smoothing Width	2
Apex Track Enables	NO
Apex Track Parameters
Peak-to-Peak Baseline Noise	Automatic
Peak width at 5% height	Automatic

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