Metabolomic data of phenolic compounds from Acer negundo extracts.

Phytochemical and metabolomic data were obtained for the most important phenolic compounds in ethanolic extracts from the endangered Acer negundo tree in Morelia, Michoacan. Samples of leaves and stems were subjected to ethanolic extraction with electric rotavapor. We developed a metabolomic analysis that encompassed the correlation between the leaf and stem extracts through principal component analysis. The data were obtained with an infinity Agilent ultrahigh resolution liquid chromatograph coupled to a Agilent triple quadrupole mass spectrometer. The protocol used was a dynamic MRM (Multiple Reaction Monitoring). Clustering result shown as heatmap (distance measure using euclidean, and clustering algorithm using ward.D).

Specifications Table

Value of the data

The data serve to identify and quantify the type and concentration of the metabolites present in the plant organs of Acer negundo.

The data collected could increase the knowledge about the level of phenolic compounds in endangered trees such as Acer negundo.

The distribution of the quantitative data could serve as a reference for metabolomic studies in other species of the genus Acer negundo.

The data of quantification of metabolites type phenolic compounds with antioxidant power in food chemistry allows the standardization of quality products from Acer negundo.

A correlation of metabolites and a database of metabolites of this species is obtained for metabolomics studies in trees of medical importance.

Currently, no metabolomic studies have been conducted on this species, and therefore it is important for studies in biochemistry, biosynthesis, plant physiology, plant biotechnology, phytochemistry and food chemistry.

Data Description

The data set in this article describes the metabolomics that includes all phenolic compounds synthesized in the leaves and stems of the Acer negundo tree. Fig. 1 describes the extraction process obtained from our protocol in which 80% ethanolic solution is used and the raw extract is obtained from a rotavaporizer. Currently, metabolomics allows the identification and quantification of total metabolites in a plant cell, or plant tissue [1], [2].

Figure 1

a) Biological sample of Acer negundo leaves and stems; b) Incorporation of the solvent c) Filtration of the samples, and d) Rotaevaporization of the solvent to obtain the raw extract.

The protocol used was a dynamic MRM (Multiple Reaction Monitoring). The conditions for each compound are described in the Table 1. The retention time variation allowed for the search of the compounds were 2 min in each case. The cell accelerator voltage was 7 V for each compound. Dilutions were made if the concentration of some compounds were higher than the linearity range.

Table 1

Conditions for the quantification of mass spectrometry data.

Compound	dMRM transition			Mass spectrometric conditions			Quantification conditions
	Precursor ion	Product ion	Retention time	Collision energy	Fragmentor	Polarity	Quantification range (µM)	Regression type	R2
Shikimic acid	173.1	111.1	0.48	10	100	Negative	0.25 - 18	Quadratic	0.99
Gallic acid	169.0	125.2	1.17	10	100	Negative	0.25 - 18	Quadratic	0.99
L-Phenylalanine	166.1	131.0	1.85	10	100	Positive	0.25 - 18	Quadratic	0.99
Protocatechuic acid	153.0	109.1	2.23	10	100	Negative	0.25 - 18	Quadratic	0.99
4-Hydroxybenzoic acid	137.1	92.8	3.43	10	100	Negative	0.25 - 18	Quadratic	0.99
Gentisic acid	153.0	109.0	3.43	10	100	Negative	0.25 - 18	Quadratic	0.99
(-)-Epigallocatechin	305.1	125.0	4.27	20	140	Negative	0.25 - 18	Quadratic	0.99
4-Hydroxyphenylacetic acid	107.1	77.0	4.5	20	140	Positive	0.25 - 18	Quadratic	0.99
(+)-Catechin	291.0	138.9	4.58	10	100	Positive	0.25 - 18	Quadratic	0.99
Vanillic acid	169.0	93.0	4.75	10	100	Positive	0.25 - 18	Quadratic	0.99
Scopolin	355.1	193.0	4.83	20	100	Positive	0.25 - 18	Quadratic	0.99
Caffeic acid	181.0	163.0	4.90	10	100	Positive	0.25 - 18	Quadratic	0.99
Chlorogenic acid	355.1	163.0	4.90	10	100	Positive	0.25 - 18	Quadratic	0.99
Malvin	655.1	331.1	5.22	40	100	Positive	0.25 - 18	Quadratic	0.99
Kuromanin	449.0	286.9	5.6	30	100	Positive	0.25 - 18	Quadratic	0.99
Procyanidin B2	577.1	425.1	5.89	10	100	Negative	0.25 - 18	Quadratic	0.99
Vanillin	153.0	124.9	6.16	10	100	Positive	0.25 - 18	Quadratic	0.99
Keracyanin	595.2	287.1	6.18	20	100	Positive	0.25 - 18	Quadratic	0.99
(-)-Epicatechin	291.0	138.8	6.44	10	100	Positive	0.25 - 18	Quadratic	0.99
Mangiferin	423.0	302.0	6.64	10	100	Positive	0.25 - 18	Quadratic	0.99
4-Coumaric acid	165.0	147.0	6.69	10	100	Positive	0.25 - 18	Quadratic	0.99
Umbelliferone	163.0	107.0	7.16	30	100	Positive	0.25 - 18	Quadratic	0.99
(-)-Gallocatechin gallate	458.9	139.0	7.29	20	80	Positive	0.25 - 18	Quadratic	0.99
Scopoletin	193.0	133.0	7.86	10	100	Positive	0.25 - 18	Quadratic	0.99
Ferulic acid	195.1	145.0	8.1	20	100	Positive	0.25 - 18	Quadratic	0.99
Quercetin 3,4-di-O-glucoside	627.0	302.9	8.18	10	100	Positive	0.25 - 18	Quadratic	0.99
3-Coumaric acid	165.0	147.0	8.49	10	100	Positive	0.25 - 18	Quadratic	0.99
Sinapic acid	225.1	207.1	8.58	10	100	Positive	0.25 - 18	Quadratic	0.99
Salicylic acid	137.0	93	8.97	10	100	Negative	0.25 - 18	Quadratic	0.99
Ellagic acid	300.5	145.0	9.0	30	170	Negative	0.25 - 18	Quadratic	0.99
Epicatechin gallate	443.1	123.0	9.36	10	100	Positive	0.25 - 18	Quadratic	0.99
Myricitrin	465.0	318.9	9.38	10	100	Positive	0.25 - 18	Quadratic	0.99
Quercetin 3-D-galactoside	465.0	302.9	9.58	10	100	Positive	0.25 - 18	Quadratic	0.99
Rutin	611.0	302.9	9.74	10	100	Positive	0.25 - 18	Quadratic	0.99
Quercetin 3-glucoside	465.0	303.0	9.91	10	100	Positive	0.25 - 18	Quadratic	0.99
Luteolin 7-O-glucoside	449.0	287.0	10.24	10	100	Positive	0.25 - 18	Quadratic	0.99
p-Anisic acid	153.1	109.0	10.26	5	120	Positive	0.25 - 18	Quadratic	0.99
2,4-Dimethoxy-6-methylbenzoic acid	197.0	179.0	11.11	5	80	Positive	0.25 - 18	Quadratic	0.99
Penta-O-galloyl-B-D-glucose	771.1	153.0	11.23	20	100	Positive	0.25 - 18	Quadratic	0.99
Kaemperol 3-O-glucoside	449.0	286.9	11.27	10	100	Positive	0.25 - 18	Quadratic	0.99
Quercitrin	449.1	303.1	11.34	10	100	Positive	0.25 - 18	Quadratic	0.99
Myricetin	317.0	179.0	11.49	10	100	Negative	0.25 - 18	Quadratic	0.99
Naringin	273.0	153.0	11.89	10	120	Positive	0.25 - 18	Quadratic	0.99
trans-Resveratrol	229.1	135.1	11.94	10	100	Positive	0.25 - 18	Quadratic	0.99
Rosmarinic acid	361.1	163.0	12.35	10	100	Positive	0.25 - 18	Quadratic	0.99
Hesperidin	609.1	301.1	12.48	20	100	Negative	0.25 - 18	Quadratic	0.99
Secoisolariciresinol	363.2	137.1	12.58	20	100	Positive	0.25 - 18	Quadratic	0.99
Phloridzin	435.0	272.9	12.81	10	100	Negative	0.25 - 18	Quadratic	0.99
trans-Cinnamic acid	149.1	131.0	13.93	10	100	Positive	0.25 - 18	Quadratic	0.99
Psoralen	187.0	131.1	14.24	20	100	Positive	0.25 - 18	Quadratic	0.99
Quercetin	302.9	153.1	14.47	35	100	Positive	0.25 - 18	Quadratic	0.99
Luteolin	287.1	153.0	14.56	30	100	Positive	0.25 - 18	Quadratic	0.99
Cirsimarin	477.0	314.9	14.93	10	100	Positive	0.25 - 18	Quadratic	0.99
Angelicin	187.0	131.1	15.03	20	100	Positive	0.25 - 18	Quadratic	0.99
Naringenin	271.0	151	16.2	10	100	Negative	0.25 - 18	Quadratic	0.99
Apigenin	271.0	153.0	16.72	30	100	Positive	0.25 - 18	Quadratic	0.99
Citropten	207.0	192.0	16.92	20	100	Positive	0.25 - 18	Quadratic	0.99
Matairesinol	359.2	137.1	17.02	10	100	Positive	0.25 - 18	Quadratic	0.99
Kaempferol	287.1	153.0	17.09	30	100	Positive	0.25 - 18	Quadratic	0.99
Hesperetin	303.1	177.1	17.5	20	100	Positive	0.25 - 18	Quadratic	0.99
Podophyllotoxin	415.1	397.1	18.68	10	100	Positive	0.25 - 18	Quadratic	0.99
Methyl cinnamate	163.1	131.0	20.92	6	100	Positive	0.25 - 18	Quadratic	0.99
Chrysin	255.1	153.0	22.53	40	100	Positive	0.25 - 18	Quadratic	0.99
Nordihydroguaiaretic acid	303.0	193.1	22.91	10	100	Positive	0.25 - 18	Quadratic	0.99
Kaempferide	301.0	258.2	24.05	20	100	Positive	0.25 - 18	Quadratic	0.99
Emodin	269.0	225.0	27.29	20	150	Negative	0.25 - 18	Quadratic	0.99
Chrysophanol	255.1	153.0	30.89	40	100	Positive	0.25 - 18	Quadratic	0.99

Phenolic compounds are powerful antioxidants [1, 2]. The 30 chemical structures of the analyzed phenolic compounds are presented in the extracts of leaves and stems of A. negundo (Fig. 2).

Figure 2

Chemical structure of the phenolic compounds analyzed in extracts of Acer negundo. 1) Shikimic acid; 2) Gallic acid; 3) L-phenylalanine; 4) Protocatechuic acid; 5) 4-Hydroxybenzoic acid; 6) Gentisic acid; 7) (-)-Epigallocatechin; 8) Caffeic acid; 9) (+)-Catechin; 10) Vanillic acid; 11) Chlorogenic acid; 12) Procyanidin B2; 13) Vanillin; 14) (-)-Epicatechin; 15) 4-Coumaric acid; 16) Scopoletin; 17) Ferulic acid; 18) Quercetin-3,4´-di-O-glucoside; 19) Sinapic acid; 20) Salicylic acid; 21) Ellagic acid; 22) Quercetin-3-D-galactoside; 23) Rutin trihydrate; 24) Quercetin-3-glucoside; 25) Luteolin-7-O-glucoside; 26) Kaempferol-3-O-glucoside; 27) Naringin; 28) Secoisolariciresinol; 29) trans-Cinnamic acid; and 30) Luteolin.

Thirty phenolic compounds were quantified, in leaf extracts there were 30 compounds and in stem extracts there were 25 compounds (Table 2).

Table 2

Concentration of phenolic compounds from A. negundo leaf and stem extracts.

Phenolic Compound				Leafs		Stems
		Molecular Formula	Molecular Weight (g/mol)	mg/g MS	Desvest	mg/g MS	Desvest
1	Shikimic acid	C7H10O5	174.15	311.64	11.93	0.00	0.00
2	Gallic acid	C7H6O5	170.12	4.10	0.23	1.86	0.07
3	L-phenylalanine	C9H11NO2	165.19	173.17	3.14	42.84	0.30
4	Protocatechuic acid	C7H6O4	154.12	1.32	0.88	1.82	0.03
5	4-Hydroxybenzoic acid	C7H6O3	138.12	8.84	0.14	2.24	0.06
6	Gentisic acid	C7H6O4	154.12	181.39	4.08	4.21	0.12
7	(-)-Epigallocatechin	C15H14O7	306.27	3.65	0.12	8.20	0.25
8	Caffeic acid	C9H8O4	180.15	1.49	0.03	0.27	0.01
9	4-Hydroxyphenylacetic acid	C8H8O3	152.14	0.00	0.00	0.00	0.00
10	(+)-Catechin	C15H14O6	290.26	5.82	0.05	65.62	1.33
11	Vanillic acid	C8H8O4	168.14	7.36	0.16	3.83	0.04
12	Scopolin	C16H18O9	354.31	0.00	0.00	0.00	0.00
13	Chlorogenic acid	C16H18O9	354.31	9.56	0.25	0.57	0.03
14	Malvin chloride	C29H35ClO17	691.03	0.00	0.00	0.00	0.00
15	Kuromanin chloride	C21H21ClO11	484.84	0.00	0.00	0.00	0.00
16	Procyanidin B2	C30H26O12	578.52	4.94	0.06	12.31	0.20
17	Vanillin	C8H8O3	152.15	6.35	0.04	3.56	0.04
18	Keracyanin chloride	C27H31ClO15	630.98	0.00	0.00	0.00	0.00
19	(-)-Epicatechin	C15H14O6	290.26	10.36	0.08	37.90	0.38
20	Mangiferin	C19H18O11	422.33	0.00	0.00	0.00	0.00
21	4-Coumaric acid	C9H8O3	164.16	5.65	0.12	1.20	0.03
22	Umbelliferone	C9H6O3	162.14	0.00	0.00	0.00	0.00
23	(-)-Gallocatechin gallate	C22H18O11	458.37	0.00	0.00	0.00	0.00
24	Scopoletin	C10H8O4	192.16	95.70	1.18	2.48	0.05
25	Ferulic acid	C10H10O4	194.18	3.98	0.08	0.90	0.03
26	Quercetin-3,4´-di-O-glucoside	C27H30O17	626.40	33.32	0.51	0.22	0.03
27	Cyanidin	C15H11O6	287.24	0.00	0.00	0.00	0.00
28	3-Coumaric acid	C9H8O3	164.16	0.00	0.00	0.00	0.00
29	Sinapic acid	C11H12O5	224.21	1.45	0.01	0.28	0.02
30	Salicylic acid	C7H6O3	138.12	32.01	1.07	5.97	0.11
31	Ellagic acid	C14H6O8	302.19	173.51	14.40	0.00	0.00
32	(-)-Epicatechin Gallate	C22H18O10	442.37	0.00	0.00	0.00	0.00
33	Myricitrin	C21H20O12	464.37	0.00	0.00	0.00	0.00
34	Pelargonidin chloride	C15H11ClO5	306.70	0.00	0.00	0.00	0.00
35	Quercetin-3-D-galactoside	C21H20O12	464.38	1557.66	25.93	99.68	1.18
36	Rutin trihydrate	C27H30O16 • 3H2O	664.56	1776.18	7.54	134.12	1.13
37	Quercetin-3-glucoside	C21H20O12	464.38	1910.18	27.08	81.27	0.84
38	Luteolin-7-O-glucoside	C21H20O11	448.38	264.11	5.34	0.00	0.00
39	p-Anisic acid	C8H8O3	152.14	0.00	0.00	0.00	0.00
40	Malvidin chloride	C17H15ClO7	366.75	0.00	0.00	0.00	0.00
41	2,4-Dimethoxy-6-methylbenzoic acid	C10H12O4	196.20	0.00	0.00	0.00	0.00
42	Penta-O-galloyl-β-D-glucose hydrate	C41H32O26 • xH2O	940.68	0.00	0.00	0.00	0.00
43	Kaempferol-3-O-glucoside	C21H20O11	448.37	4238.41	27.55	34.87	0.45
44	Quercitrin	C21H20O11	448.38	0.00	0.00	0.00	0.00
45	Myricetin	C15H10O8	318.24	0.00	0.00	0.00	0.00
46	Naringin	C27H32O14	580.54	9.60	0.30	0.00	0.00
47	trans-Resveratrol	C14H12O3	228,25	0.00	0.00	0.00	0.00
48	Rosmarinic acid	C18H16O8	360,31	0.00	0.00	0.00	0.00
49	Hesperidin	C28H34O15	610,18	0.00	0.00	0.00	0.00
50	Secoisolariciresinol	C20H26O6	362.17	16.18	0.15	0.58	0.06
51	Phloridzin	C21H24O10	436.413	0.00	0.00	0.00	0.00
52	trans-Cinnamic acid	C9H8O2	148.16	0.44	0.01	0.32	0.01
53	Psoralen	C11H6O3	186.16	0.00	0.00	0.00	0.00
54	Quercetin	C15H10O7	302,236	0.00	0.00	0.00	0.00
55	Luteolin	C15H10O6	286.24	41.27	0.94	0.00	0.00
56	Cirsimarin	C23H24O11	476.4	0.00	0.00	0.00	0.00
57	Angelicin	C11H6O3	186.166	0.00	0.00	0.00	0.00
58	Naringenin	C15H12O5	272,25	0.00	0.00	0.00	0.00
59	Apigenin	C15H10O5	270.05	0.00	0.00	0.00	0.00
60	Citropten	C11H10O4	206.19	0.00	0.00	0.00	0.00

Fig. 3 shows a heat map of differential metabolites found by metabolomic analysis. The blue color represents the decreasing trend, the red represents an increasing trend.

Figure 3

Clustering result shown as heatmap (distance measure using euclidean, and clustering algorithm using ward.D).

Fig. 4 shows the paired scorecards between the selected main components (PCs). The explained variance of each PC is shown in the corresponding diagonal cell.

Figure 4

Pairwise score plots between the selected PCs.

Fig. 5 shows a score chart between the selected main components (PCs). The variations explained are shown in brackets.

Figure 5

Scores plot between the selected PCs.

In Fig. 6 a 3D score plot is shown between the selected main components (PCs). The explained variations are shown in brackets.

Figure 6

3D score plot between the selected PCs.

Fig. 7 shows a load plot for the selected main components (PCs).

Figure 7

Loadings plot for the selected PCs.

Fig. 8 shows a biplot of the main components among the selected PCs.

Figure 8

PCA biplot between the selected PCs.

Experimental Design, Materials, and Methods

Extraction data acquisition

The samples come from an Acer negundo mother tree free of pests and diseases. Ten leaf and stem samples of A. negundo were collected and then subjected to a dehydration process that required three days (72 h) a temperature of 50 °C. Then 100 mg of dry matter was dissolved in 100 mL of 80% ethanol. The mixture was filtered using Whatman No. 1 filter paper. To obtain the raw extracts, a rotary evaporator was used.

Identification and quantification of phenolic compounds

The identification and quantification of phenolic compounds was performed basically as it was previously reported in Juárez-Trujillo et al., 2018 [3] and Monribot et al., 2019 [4]. The equipment used was a UPLC coupled to a triple quadrupole mass spectrometer. The equipment was injected with 2 µL of ethanolic extract from leaves and 2 µL of ethanolic extract from stems.

Sample preparation

Samples were filtered with 0.5 μm PTFE membranes and placed in 2 mL UPLC vials.

Chromatographic conditions

The data were obtained with a 1290 infinity Agilent ultrahigh resolution liquid chromatograph coupled to a 6460 Agilent triple quadrupole mass spectrometer. The mobile phases were water with 0.1% of formic acid (A) and acetonitrile with 0.1% formic acid (B), both in MS grade. The gradient elution profile is presented in the Table 3.

Table 3

 

Time (min)	Solution A (%)	Solution B (%)
0	99	1
30	50	50
35	1	99
39	1	99
40	99	1
45	99	1

The flow was 0.3 mL/min. The injection volume was 2 µL. The column was a Waters, BEH, 2.1 × 50 mm, 1.7 Microns. The column temperature was 40 °C.

Mass spectrometry conditions

The conditions of mass spectrometry is presented in the Table 4.

Table 4

 

Parameter	Value
Gas Temp	300 oC
Gas Flow	5 L/min
Nebulizer	45 psi
Sheath Gas Temp	250 oC
Sheath Gas Flow	11 L/min
Capillary voltage (positive and negative)	3500 V
Nozzle voltage (positive and negative)	500 V

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships which have, or could be perceived to have, influenced the work reported in this paper.

Supplementary materials

Supplementary material associated with this article can be found, in the online version, at http://dx.doi.org/10.17632/hhp8z52n9t.2 (Mendeley Data).

Subject	Botany, Phytochemistry, Plant biotechnology, Metabolomics, Food chemistry, Chemistry of natural products.
Specific subject area	Metabolomic analysis, liquid chromatography, mass spectrometry.
Type of data	Table, Figure, Image
How data were acquired	Leaf sample collection, stem sample collection, liquid chromatography, mass spectrometry.
Data format	Raw and Analysed
Parameters for data collection	Samples of leaves and stems of Acer negundo tree were collected and subjected to a dehydration process that required three days at a temperature of 50 °C in rotary evaporator.
Description of data collection	A botanical exploration of the samples was conducted to obtain the ethanolic extracts. The samples were filtered and then the solvent was evaporizated in an electric rotavapor to obtain the crude extracts. The samples were collected for metabolomic analysis by liquid chromatography and mass spectrometry. Identification and quantification of the analyzed phenolic compounds in leaf and stem extracts were obtained. A heat map was obtained. The equipment used was a UPLC coupled to a triple quadrupole mass spectrometer. The equipment was injected with 2 µL of ethanolic extract from leaves and 2 µL of ethanolic extract from stems.
Data source location	Morelia, Michoacán, MéxicoCountry: MéxicoThe GPS coordinates are Latitude and longitude for collected samples/data: West, 1920 m.a.s.l.
Data accessibility	Repository name: Mendeley DataData identification number: 2 Direct URL to data: http://dx.doi.org/10.17632/hhp8z52n9t.2