Table 1 Metabolites with statistical significance in the two phases of the fermentation process identified by metabolic fingerprinting using LC-QTOF-MS( ±) and GC-QTOF-MS( +).

From: Dissecting fine-flavor cocoa bean fermentation through metabolomics analysis to break down the current metabolic paradigm

Compound name	Molecular Formula	Molecular weight (DB) g/mol	RT (min)	Mass error (ppm)	Analytical platform	DET	CON	CV in QC (%)	Fold Change	VIP Value	p-value with FDR
*Amino acids, peptides, and derivatives*
Alanine	C₃H₇NO₂	89.0476	7.553	–	GC-QTOF-MS	EI	Identified	1.85	1.3	1.098	0.0034
Aspartic acid	C₄H₇NO₄	133.0375	8.11	7	LC-QTOF-MS	ESI-	Putative	1.25	6.6	2.650	0.00019
Glutamic acid	C₅H₉NO₄	47.1293	14.55	–	GC-QTOF-MS	EI	Identified	2.9	2.1	1.34247	–
Glutamine	C₅H₁₀N₂O₃	146.0691	1.81	3	LC-QTOF-MS GC-QTOF-MS	ESI + EI	Putative Identified	1.25	5.3	2.336	7.22 E−05
Leucine	C₆H₁₃NO₂	131.0946	2.08	5	LC-QTOF-MS	ESI-	Putative	2.57	3.7	1.524	9.58 E−05
Phenylalanine	C₉H₁₁NO₂	165.079	3.44	2	LC-QTOF-MS GC-QTOF-MS	ESI + EI	Putative Identified	2.42	3.3	1.537	9.58 E−05
Proline	C₅H₉NO₂	115.0633	2.69	5	LC-QTOF-MS GC-QTOF-MS	ESI + EI	Putative Identified	13.58	3.3	1.790	0.00011
Serine	C₃H₇NO₃	105.0926	11.32	–	GC-QTOF-MS	EI	Identified	3.3	5.1	1.61403	–
Threonine	C₄H₉NO₃	119.1192	11.69	–	GC-QTOF-MS	EI	Identified	1.4	5.4	1.6294	–
Tyramine	C₈H₁₁NO	137.0841	2.81	2	LC-QTOF-MS	ESI +	Putative	2.88	4.6	1.839	7.22 E−05
Tyrosine	C₉H₁₁NO₃	181.0739	1.83	3	LC-QTOF-MS	ESI-	Putative	2.57	2.5	1.424	8.61 E−07
Caffeoyl aspartic acid	C₁₃H₁₃NO₇	295.0692	8.12	2	LC-QTOF-MS	ESI-	Putative	1.78	8.8	3.820	0.00019
AlanylProline	C₈H₁₄N₂O₃	186.1004	2.26	2	LC-QTOF-MS	ESI +	Putative	7.00	7.0	2.000	9.59 E−09
ArginylProline	C₁₁H₂₁N₅O₃	271.1644	1.94	6	LC-QTOF-MS	ESI +	Putative	4.03	28.8	1.627	7.22 E−05
Glutamylglutamine	C₁₀H₁₇N₃O₆	275.1117	1.9	0	LC-QTOF-MS	ESI-	Putative	1.99	11.7	1.161	9.10 E−05
Glutamylleucine	C₁₁H₂₀N₂O₅	260.1372	2.07	2	LC-QTOF-MS	ESI ±	MS/MS	1.42	6.1	1.744	7.22 E−05
LeucylThreonine	C₁₀H₂₀N₂O₄	232.1423	1.72	2	LC-QTOF-MS	ESI +	Putative	2.44	2.5	1.561	0.00021
ProlylLysine	C₁₁H₂₁N₃O₃	243.1583	2.52	2	LC-QTOF-MS	ESI-	Putative	3.17	6.4	1.794	9.10 E−05
ProlylSerine	C₈H₁₄N₂O₄	202.0954	2.07	2	LC-QTOF-MS	ESI +	Putative	1.90	26.0	2.170	7.22 E−05
Tripeptide 1	C₁₇H₂₉N₇O₅	411.223	1.64	7	LC-QTOF-MS	ESI ±	Putative	1.80	10.0	2.162	7.22 E−05
Tripeptide 2	C₁₃H₂₅N₃O₅	303.1794	1.88	0	LC-QTOF-MS	ESI ±	Putative	1.61	2.6	1.649	0.00086
Tripeptide 3	C₁₆H₂₉N₅O₇	403.2067	1.93	1	LC-QTOF-MS	ESI ±	Putative	1.52	12.6	2.848	7.22 E−05
Tripeptide 4	C₁₇H₂₂N₄O₈	410.1438	3.28	0	LC-QTOF-MS	ESI-	Putative	3.43	9.7	1.052	9.10 E−05
*Organic acids*
Avenanthramide 2	C₁₈H₁₇NO₇	359.1005	11.98	2	LC-QTOF-MS	ESI-	Putative	3.38	14.5	1.187	9.58 E−05
Benzoic acid	C₇H₆O₂	122.0368	11.39	5	LC-QTOF-MS	ESI +	Putative	1.42	12.6	2.364	0.00013
Caffeic acid	C₉H₈O₄	180.0423	8.1	2	LC-QTOF-MS	ESI +	MS/MS	0.86	4.8	4.299	0.00016
Coumaric acid	C₉H₈O₃	164.0473	11.39	4	LC-QTOF-MS	ESI +	MS/MS	2.07	10.0	1.888	0.00013
Oxoglutaric acid	C₅H₆O₅	146.0215	1.58	5	LC-QTOF-MS	ESI-	Putative	6.36	1.5	1.079	3.99 E−05
Salicylic acid	C₇H₆O₃	138.0317	11.4	3	LC-QTOF-MS	ESI-	Putative	2.08	13.8	1.691	0.00015
Sesamol	C₇H₆O₃	138.0317	11.39	4	LC-QTOF-MS	ESI ±	Putative	1.28	10.3	3.352	0.00013
Tetrahydroxychalcone 4'-O-(2''-O-acetyl-6''-O-cinnamoyl)glucoside	C₃₂H₃₀O₁₂	606.1737	12.64	1	LC-QTOF-MS	ESI-	Putative	3.81	14.1	1.434	9.10 E−05
Tumonoic Acid H	C₂₆H₄₅NO₇	483.3196	4.62	5	LC-QTOF-MS	ESI +	Putative	3.06	12.2	2.671	7.20 E−05
*Carbonyl compounds*
Acetophenone	C₈H₈O	120.0575	12.26	6	LC-QTOF-MS	ESI-	Putative	2.51	6.8	1.271	0.0011
Acetol	C₃H₆O₂	74.0785	13.29		GC-QTOF-MS	EI	Identified	1.7	5.6	1.23759	0.0001
Hydroxyacetophenone	C₈H₈O₂	136.0524	8.11	6	LC-QTOF-MS	ESI-	Putative	2.04	6.1	1.877	0.00015
*Carbohydrates*
Anhydrofructose	C₆H₁₀O₅	162.0528	1.16	4	LC-QTOF-MS	ESI +	Putative	6.46	0.2	1.540	7.22 E−05
Arabitol//Ribitol	C₅H₁₂O₅	152.0685	15.59	–	GC-QTOF-MS	EI	Identified	0.0	2.0	1.04962	0.00016
Decarboxybetanin	C₂₃H₂₇N₂O₁₁	507.1615	4.42	4	LC-QTOF-MS	ESI-	Putative	1.63	15.0	1.158	9.10 E−05
Dihydrocaffeic acid 3-O-glucuronide	C₁₅H₁₈O₁₀	358.09	1.14	2	LC-QTOF-MS	ESI +	MS/MS	2.33	0.3	2.240	5.04 E−06
Dihydroxyphenyl 1-O-(6-O-galloyl-beta-D-glucopyranoside)	C₁₉H₂₀O₁₂	440.0955	1.14	5	LC-QTOF-MS	ESI-	Putative	1.39	0.3	1.271	0.00015
Gluconic acid	C₆H₁₂O₇	196.0583	1.13	6	LC-QTOF-MS	ESI-	Putative	1.27	0.7	2.212	–
Glucose //Galactose	C₆H₁₂O₆	180.0634	17.61	–	GC-QTOF-MS	EI	Identified	2.6	2.1	1.46337	–
Maltose	C₁₂H₂₂O₁₁	342.2965	24.86	–	GC-QTOF-MS	EI	Identified	4.7	0.0	1.07032	–
Mannitol	C₆H₁₄O₆	182.1718	17.8	–	GC-QTOF-MS	EI	Identified	3.8	0.8	–	0.0178867
Raffinose	C₁₈H₃₂O₁₆	504.169	1.13	1	LC-QTOF-MS	ESI-	Putative	1.70	0.1	2.429	1.22 E−05
Ribose // Lyxose // Arabinose	C₅H₁₀O₅	150.0528	15.1	–	GC-QTOF-MS	EI	Identified	1.4	1.3	1.17136	–
Sorbitol	C₆H₁₄O₆	182.1718	17.86	-	GC-QTOF-MS	EI	Identified	3.5	0.8	1.2679	–
Sorbosone	C₆H₁₀O₆	178.0477	1.21	6	LC-QTOF-MS	ESI-	Putative	2.87	0.5	1.040	0.00019
Stachyose // Maltotetraose	C₂₄H₄₂O₂₁	666.2219	1.1	0	LC-QTOF-MS	ESI-	Putative	1.68	0.2	2.581	1.09 E−07
*Phenols*
Catechol	C₆H₆O₂	110.1106	10.59		GC-QTOF-MS	EI	Identified	2.8	1.5	1.22319	0.011
Dopamine	C₈H₁₁NO₂	153.079	10.11	3	LC-QTOF-MS	ESI +	Putative	3.11	6.1	1.570	7.22 E−05
Methylcatechol	C₇H₈O₂	124.0524	11.4	6	LC-QTOF-MS	ESI-	Putative	2.31	11.9	1.249	0.00015
Phenol	C₆H₆O	94.0419	3.42	8	LC-QTOF-MS	ESI +	Putative	2.23	2.5	2.902	8.70 E−05
Pyrocatechol	C₆H₆O₂	110.0368	11.4	6	LC-QTOF-MS	ESI-	Putative	2.88	12.3	1.234	0.00015
Vanillin	C₈H₈O₃	152.0473	8.1	3	LC-QTOF-MS	ESI +	MS/MS	1.29	5.3	2.567	0.00016
Vanillin isobutyrate	C₁₂H₁₄O₄	222.0892	11.4	3	LC-QTOF-MS	ESI-	Putative	1.44	12.7	1.213	0.00015
*Indoles and derivatives*
Indolamine	C₈H₈N₂	132.0687	8.12	3	LC-QTOF-MS	ESI-	Putative	8.33	4.7	1.840	0.00019
Indoleacrylic acid	C₁₁H₉NO₂	187.0633	10.2	3	LC-QTOF-MS	ESI +	Putative	1.93	8.5	1.808	7.22 E−05
*Phenylpropanoids*
Schizandrin	C₂₄H₃₂O₇	432.2148	10.91	7	LC-QTOF-MS	ESI ±	Putative	1.18	6.8	2.963	7.20 E−05
Sinapine	C₁₆H₂₄NO₅	310.1654	6.58	3	LC-QTOF-MS	ESI-	Putative	1.93	15.5	1.195	9.10 E−05
*Pyridine nucleotides*
Nicotinamide ribotide	C₁₁H₁₅N₂O₈P	334.0566	10.39	8	LC-QTOF-MS	ESI-	Putative	1.55	10.1	1.582	0.00024
*Coumarins*
Coumarin	C₉H₆O₂	146.0368	10.47	4	LC-QTOF-MS	ESI +	MS/MS	1.56	1.7	1.756	0.011
Methylcoumarin	C₁₀H₈O₂	160.0524	11.4	4	LC-QTOF-MS	ESI-	Putative	1.38	12.7	1.293	0.00015
Marmesin	C₁₄H₁₄O₄	246.0892	9.44	2	LC-QTOF-MS	ESI-	Putative	5.47	16.6	1.452	9.10 E−05
Occidentoside	C₃₆H₃₂O₁₅	704.1741	1.09	6	LC-QTOF-MS	ESI +	MS/MS	1.35	0.3	2.482	1.19 E−07
*Flavonoids*
Alkannin	C₁₆H₁₆O₅	288.0998	12.48	1	LC-QTOF-MS	ESI +	Putative	3.67	3.0	1.649	0.0022
Arecatannin A2	C₆₀H₅₀O₂₄	1154.2692	12.09	2	LC-QTOF-MS	ESI-	Putative	2.14	0.7	1.224	0.044
Arecatannin A3	C₇₅H₆₂O₃₀	1442.3326	12.03	2	LC-QTOF-MS	ESI-	Putative	2.43	0.7	1.576	0.021
A-type procyanidin dimer	C₃₀H₂₄O₁₂	576.1268	13.86	0	LC-QTOF-MS	ESI-	Putative	1.56	1.9	1.050	0.0045
A-type procyanidin dimer	C₃₀H₂₄O₁₂	576.1268	12.48	1	LC-QTOF-MS	ESI +	Putative	1.53	3.1	1.635	0.00086
B-type procyanidin dimer	C₃₀H₂₆O₁₂	578.1424	10.93	0	LC-QTOF-MS	ESI-	Putative	1.96	4.2	5.049	0.00081
B-type procyanidin dimer	C₃₀H₂₆O₁₂	578.1424	11.15	0	LC-QTOF-MS	ESI-	Putative	2.17	4.9	2.153	0.00054
B-type procyanidin dimer	C₃₀H₂₆O₁₂	578.1424	12.48	1	LC-QTOF-MS	ESI ±	MS/MS	1.29	3.1	1.586	0.0011
C-type procyanidin trimer	C₄₅H₃₈O₁₈	866.2058	10.9	4	LC-QTOF-MS	ESI-	Putative	1.49	2.5	2.042	0.0031
Butein -arabinosyl-galactoside	C₂₆H₃₀O₁₄	566.1636	1.12	9	LC-QTOF-MS	ESI-	Putative	1.75	0.3	1.318	4.91 E−08
Caffeoylpelargonidin 5-glucoside	C₃₀H₂₇O₁₃	595.1452	12.09	2	LC-QTOF-MS	ESI-	Putative	1.41	0.8	1.146	–
Catechin	C₁₅H₁₄O₆	290.079	11.39	2	LC-QTOF-MS	ESI ±	MS/MS	2.03	12.5	2.733	0.00013
Epicatechin	C₁₅H₁₄O₆	290.079	12.48	4	LC-QTOF-MS GC-QTOF-MS	ESI- EI	Putative Identified	1.76	3.1	1.110	0.00012
Epicatechin 3-glucoside	C₂₁H₂₄O₁₁	452.1319	8.66	1	LC-QTOF-MS	ESI-	Putative	3.16	5.9	1.176	0.00029
Epigallocatechin 3-O-(4-hydroxybenzoate)	C₂₂H₁₈O₉	426.0951	10.93	2	LC-QTOF-MS	ESI-	Putative	2.06	4.3	1.824	0.00081
Isoflavonoid O-glycosides	C₂₈H₃₄O₁₂	562.205	11.26	4	LC-QTOF-MS	ESI-	Putative	1.03	7.2	1.460	9.10 E−05
Kaempferol -diacetyl-coumarylrhamnoside	C₃₄H₃₀O₁₄	662.1636	12.74	2	LC-QTOF-MS	ESI-	Putative	3.25	2.4	1.324	0.0017
Kaempferol-caffeoylglucosyl-rhamnoside	C₃₆H₃₆O₁₈	756.1902	12.59	1	LC-QTOF-MS	ESI-	Putative	2.33	2.2	1.329	0.0017
Viscumneoside V	C₃₂H₄₀O₁₉	728.2164	1.11	6	LC-QTOF-MS	ESI-	Putative	2.02	0.4	1.378	1.36 E−08
*Purines and purine derivatives*
Hydroxyadenine // Guanine	C₅H₅N₅O	151.0494	1.96	3	LC-QTOF-MS	ESI +	MS/MS	1.08	3.1	3.264	7.22 E−05
Xanthine	C₅H₄N₄O₂	152.0334	1.96	2	LC-QTOF-MS	ESI +	Putative	1.66	3.7	1.660	7.22 E−05
*Organoheterocyclic compound*
Cytosine	C₄H₅N₃O	111.0433	1.21	6	LC-QTOF-MS	ESI +	MS/MS	1.74	3.9	2.042	2.00 E−12
Maltol	C₆H₆O₃	126.0317	11.4	4	LC-QTOF-MS	ESI-	Putative	7.79	9.7	1.239	0.00015
*Terpenoids*
Cedrol	C₁₅H₂₆O	222.1984	10.59	4	LC-QTOF-MS	ESI +	Putative	1.83	7.7	1.941	7.22 E−05
Irone	C₁₄H₂₂O	206.1671	10.69	5	LC-QTOF-MS	ESI +	Putative	1.58	35.7	3.768	7.22 E−05
Salannin	C₃₄H₄₄O₉	596.2985	18.8	5	LC-QTOF-MS	ESI-	Putative	4.87	4.0	1.836	9.58 E−05
*Glycosides*
Methylthiooctyl-desulfoglucosinolate	C₁₆H₃₁NO₆S₂	397.1593	4.15	0	LC-QTOF-MS	ESI-	Putative	2.22	1.2	1.029	0.0082
*Phenylpropanoids and polyketides*
Resveratrol 3-sulfate	C₁₄H₁₂O₆S	308.0355	11.94	0	LC-QTOF-MS	ESI-	Putative	1.34	5.1	1.150	0.00066
Oleandolide	C₂₀H₃₄O₇	386.4798	4.22	5	LC-QTOF-MS	ESI +	Putative	1.38	32.8	2.074	7.20 E−05
*Fatty acyls*
Heptadecanoic acid	C₁₇H₃₄O₂	268.4348	19.81		GC-QTOF-MS	EI	Identified	2.7	1.3	–	0.00022
Hydroxyandrostane-3-glucuronide	C₂₅H₄₀O₉	484.2672	2.54	3	LC-QTOF-MS	ESI ±	Putative	0.76	5.4	3.033	7.22 E−05
hydroxy-tetradecenoic acid	C₁₄H₂₆O₃	242.1882	11.87	9	LC-QTOF-MS	ESI-	Putative	3.44	9.4	1.235	9.58 E−05
Keto-decanoylcarnitine	C₁₇H₃₁NO₅	329.2202	11.6	7	LC-QTOF-MS	ESI-	Putative	1.94	3.9	1.062	0.00021
Linalool xylosyl-glucoside	C₂₁H₃₆O₁₀	448.2308	5.96	4	LC-QTOF-MS	ESI ±	Putative	1.85	57.7	3.051	7.20 E−05
Methylbutanoyl)-6-apiosylglucose	C₁₆H₂₈O₁₁	396.1632	4.31	1	LC-QTOF-MS	ESI-	Putative	6.42	1.8	1.053	0.00049
Methylmalate	C₅H₈O₅	148.0372	1.15	7	LC-QTOF-MS	ESI-	Putative	1.62	0.5	1.532	0.00015
Myristic acid	C₁₄H₂₈O₂	228.3709	16.94	–	GC-QTOF-MS	EI	Identified	2.5	1.3	–	0.0051
Oleic acid	C₁₈H₃₄O₂	282.4614	20.47	–	GC-QTOF-MS	EI	Identified	12.0	1.3	1.03152	-
Stearic acid	C₁₈H₃₆O₂	284.4772	20.68	–	GC-QTOF-MS	EI	Identified	2.7	1.2	1.24361	-
*Lipids*
Deoxyestradiol	C₁₈H₂₄O	256.1827	11.87	4	LC-QTOF-MS	ESI ±	Putative	1.90	11.6	2.035	7.22 E−05
LPC(14:0)	C₂₂H₄₄NO₈P	481.2805	13.35	4	LC-QTOF-MS	ESI-	Putative	1.05	17.3	1.689	9.10 E−05
LPC(18:2)	C₂₆H₅₀NO₇P	519.3325	19.92	1	LC-QTOF-MS	ESI +	MS/MS	5.83	5.6	3.004	0.00011
LPC(O-18:1)	C₂₆H₅₂NO₇P	521.3481	21.21	1	LC-QTOF-MS	ESI +	MS/MS	5.20	4.2	2.800	0.00031
Palmitoyl 3-carbacyclic Phosphatidic Acid	C₂₀H₃₉O₅P	390.2535	10.19	7	LC-QTOF-MS	ESI +	Putative	3.58	16.1	2.141	7.22 E−05
PI(18:1)	C₂₇H₅₁O₁₂P	598.3118	20	2	LC-QTOF-MS	ESI-	Putative	16.18	2.0	1.061	0.0072
PS(21:0)	C₂₇H₅₄NO₉P	567.3536	21.26	3	LC-QTOF-MS	ESI-	Putative	15.59	2.7	1.082	0.0012
Sphinganine	C₁₈H₃₉NO₂	301.2981	18.83	2	LC-QTOF-MS	ESI +	MS/MS	3.08	0.6	1.653	0.00016
Sulfoglycolithocholate	C₂₆H₄₂NO₇S	512.2682	6.05	5	LC-QTOF-MS	ESI ±	Putative	1.85	35.0	2.272	7.22E−05

^aDET: detection mode; ^bCV, coefficient of variation of metabolites in QC samples; ^cVIP, Variable importance in projection; ^dCON: Confirmation; ^e p-value obtained after Benjamini–Hochberg correction test.
LC Liquid Chromatography, QTOF-MS quadrupole time-of-flight mass spectrometry.

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Table 1 Metabolites with statistical significance in the two phases of the fermentation process identified by metabolic fingerprinting using LC-QTOF-MS( ±) and GC-QTOF-MS( +).

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