5. Metabolomics: definitions
What can the cell potentially do?
What is currently being turned on?
What enzymes are currently active?
What is being produced/consumed?
System biology
6. Metabolomics: definitions
metabolomics is the "systematic study of the unique chemical fingerprints that
specific cellular processes leave behind", the study of their small-molecule
metabolite profiles (Daviss 2005)
metabolomics is a newly emerging field of "omics" research concerned with the
comprehensive characterization of the small molecule metabolites in biological
systems. (Metabolomics Society)
metabolomics is the comprehensive and holistic study of the metabolome
the complete set of small-molecule
metabolites to be found within a biological
sample
metabonome: the complete set of metabologically
regulated elements in cells
12. Wine Chemistry – Wine Composition
How big is the wine metabolome?
13. Metabolomic: what is and what is not
How big is the metabolome?
Sigma-Aldrich has ~55K commercial available chemicals
Kegg contains 18K metabolites
HMDB is based in ~42K metabolites
Plant metabolome is estimated to cover 200K metabolites
PubChem ID contains more than 10M entries
CAS contains over 90M unique organic
and inorganic chemicals
ChemSpider contains over 57M
compounds from 530 data sources
14. Plant metabolome is estimated to cover
200 000 metabolites
#ofmetabolites5-21% ethanol
g/L
mg/L
µg/L
ng/L
pg/L
fg/L
How big is the metabolome?
Wine Chemistry – Wine Composition
18. Lisec et al. Anal Chem 2016
Currently, the best dynamic range of modern MS is 106
approximately and is significantly lower than the estimated
concentration range of cellular metabolites as 1012 or more (Lei
et al JBC 2011)
Metabolomics: what is and what is not
22. Grape Sensorial analysis: grape
Aromatic grape
Moscato, Gewϋrztraminer
Wine smell as the grape
Non-aromatic grape
a) silenced and b) not-silenced
Sauvignon blanc
Must non-aromatic, wine aromatic
23. Grape Sensorial analysis: grape
aromatic part aromatic part
sugar
O
OOH
OH
OH
OH
OH
enzymatic
or chemical
hydrolysis
24. Grape aromatic compounds: terpenoids
Isoprene
Hydrocarbon
5 x Carbons
2 x Isoprene
Monoterpenes
10 x Carbons
3 x Isoprene
Sesquiterpene
15 x Carbons
4 x Isoprene
Diterpenes
20 x Carbons
5 x Isoprene
Sesteterpenes
25 x Carbons
6 x Isoprene
Triterpenes
25 x Carbons
Terpene + Oxygen or Nitrogen = terpenoids
26. Grape aromatic compounds: volatiles thiols
O
SH
OH
SH
O
SHO
4-mercapto-4-methylpentan-2-one
4MMP
3-mercaptohexan-1-ol
3MH
3-mercaptohexyl-acetate
3MHA
46. OH
OH
OH
Must sensorial analysis: alcoholic fermentation / Ehrlich reaction
phenyl-ethanol 3-methyl-butanol 2-methyl-butanol
volatiles
threshold
300 mg/L
Adolf and Versini, 1999
47. Must sensorial analysis: alcoholic fermentation
OH
O
O
O OH
OH
OH
OH
OH
O
O
OH
O
glucose
pyruvic acid acetaldehyde ethanol
O
OH
acetic acid
48. Must sensorial analysis: alcoholic fermentation
O
OH
acetic acid
OH
O
OH
O
OH
O
OH
O
OH
O
2-methylpropanoic acid
3-methylbutanoic
octanoic acid acid
(caprilic acid)
Hexanoic acid
(capronic acid)
butanoic acid
(butyric acid)
OH
Odecanoic acid acid
(caprinic acid)
49. Must sensorial analysis: alcoholic fermentation / half time
OH
O
OH
O
OH
O
OH
O
3-methylbutanoic
octanoic acid acid
(caprilic acid)
Hexanoic acid
(capronic acid)
butanoic acid
(butyric acid)
O
O
O
O
O
O
O
O
isoamyl acetate
ethyl butanoate
ethyl hexanoate
ethyl octanoate
50. Wine sensorial analysis: the first battle
O
O
O
O
O
O
ethyl butanoate
ethyl hexanoate
ethyl octanoate
O
O
isoamyl acetate
OH
OH
OH
phenyl-ethanol
3-methyl-butanol
2-methyl-butanol
superior alcohol versus esters
51. Wine sensorial analysis: the first battle
O
O
O
O
O
O
ethyl butanoate
ethyl hexanoate
ethyl octanoate
O
O
isoamyl acetate
OH
OH
OH
phenyl-ethanol
3-methyl-butanol
2-methyl-butanol
superior alcohol versus esters
52. Wine sensorial analysis: the first battle
O
O
O
O
O
O
ethyl butanoate
ethyl hexanoate
ethyl octanoate
O
O
isoamyl acetate
OH
OH
OH
phenyl-ethanol
3-methyl-butanol
2-methyl-butanol
superior alcohol versus esters
65. Grape Sensorial analysis: human perception
Primary gustatory cortex
Working memory and
behavioral strategies
Primary gustatory cortex and emotion Primary gustatory/olfactory cortex and memory
68. Wine Chemistry – Phenolics – Classification according the skeleton
C6 C6-C3 C6-C3-C6
O
OH
O
OH
C6-C2-C6
phenolic acids cinnamics acids stilbenoids flavanoids
O
OH
OH
O
OH
OH
OH
O
OH
OH
OH
OH
OH
OH
OH
O
OH
OH
OH
O
OH
OH
O
OH
OH
OH
OH
OH
OH
OH
OH
O
OH
OH
OH
O
OH
OH
O
OH
O
69. Wine Chemistry – Phenolics – Phenolic acids
shikimic acid
O
OH
OH
O
OH
OH
OH
O
OH
OH
OH
OH
gallic acid
UV-Vis spectrum
nm250 300 350 400 450 500 550
270 nm
nm250 300 350 400 450 500 550
280 nm
• Wooden barrel
• Non vinifera
• Hydrolysable tannins
gallic acid
O
HO
HO
OH
O
HO
O
OH
OH
OH
glucogallin
74. fertaric acid
Wine Chemistry – Phenolics - Cinnamates
coutaric acid 4-vinyl phenol
4-vinyl guaicol 4-ethyl guaicol
4-ethyl phenol
OH
O
O
OH
O
OH
OH
O
OH
O
O
OH
O
OH
OH
O
O CH3
OH
CH2
O CH3
OH
CH3
O CH3
OH
CH3OH
CH2
81. Wine Chemistry – Phenolics - Anthocyanins
O
+
OH
OH
O
OH
O
OO
OH
OH
OH
OH
O O
OH
OH
OH
OH
O
+
OH
O
OH
O
OO
OH
OH
OH
OH
OH
O
+
OH
O
OH
O
OO
OH
OH
OH
O
O
OH
OH
O
+
OH
O
OH
O
OO
OH
OH
OH
O
O
OH
OH
OH
O
+
OH
O
OH
O
OO
OH
OH
OH
O
O
OH
O
+
OH
O
OH
O
OH
82. Wine Chemistry – Phenolics - Anthocyanins
OH
OOH
OH
OH
OH
OH
O
+
OH
O
OH
O
OO
OH
OH
OH
OH
O
+
O
OH
OH
O
O OH
OH
OH
OH
OH
O
OH
O
OH
OH
OH
OH
O
+
O
OH
OH
O
O
OH
OH
OH
OH
O
OH
OH
O
OH
OH
OH
OH
O
+
OH
OH
O
OH
O
OO
OH
OH
OH
OH
83. Wine Chemistry – Phenolics - Anthocyanins
O
+
OH
OH
O
OH
O
OO
OH
OH
OH
OH
O
+
O
OH
OH
O
O OH
OH
OH
OH
O
O
O
+
O
OH
OH
O
O OH
OH
OH
OH
O
O OH
O
O
+
OH
O
OH
O
OO
OH
OH
OH
OH
OH
p-coumaric acid
86. Wine Chemistry – Phenolics - Anthocyanins
Bobeica et al Frontiers 2016
87. Mattivi et al JAFC 2006
cyanidin
delphinidin
pelargonidin
malvidin
petunidin
Wine Chemistry – Phenolics - Anthocyanins
88. Wine Chemistry – Phenolics - Anthocyanins
O
+
O
OH
OH
OH
O
O OH
OH
OH
OH
O O
+
OH
OH
OH
OH
O
O OH
OH
OH
OH
OH
O
+
O
OH
OH
OH
O
O OH
OH
OH
OH
O
+
OH
OH
OH
OH
O
O OH
OH
OH
OH
O
+
O
OH
OH
OH
O
O OH
OH
OH
OH
OH
+
+ +
93. DAD trace at
520 nm
mlv 3-glu vitisin B
mlv p-coum 3-glu
pinotins
Wine Chemistry – Phenolics - Anthocyanins
94. DO WHITE GRAPES REALLY EXIST?
6.00 6.50 7.00 7.50
%100
Cabernet
Sauvignon
Arapitsas et al Food Res Inter 2014
95. DO WHITE GRAPES REALLY EXIST?
6.00 6.50 7.00 7.50
%100
%
100
6.00 6.50 7.00
Chardonnay
Riesling
Sauvignon B.
Gewürztraminer
Muscateller
Cabernet
Sauvignon
Arapitsas et al Food Res Inter 2014
96. DO WHITE GRAPES REALLY EXIST?
Arapitsas et al Food Res Inter 2014
99. O
+
O
OH
OH
OH
O
O OH
OH
OH
OH
O O
+
OH
OH
OH
OH
O
O OH
OH
OH
OH
OH
O
+
O
OH
OH
OH
O
O OH
OH
OH
OH
O
+
OH
OH
OH
OH
O
O OH
OH
OH
OH
O
+
O
OH
OH
OH
O
O OH
OH
OH
OH
OH
+
+ +
Pigments & Wine ageing
Arapitsas et al J Agric Food Chem 2012
143. Arapitsas et al. Scientific Reports 2018
Wine Chemistry – Phenolics – Flavanols
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
epicatechin
procyanidin B2
ECAT-SO3H
epicatechin-SO3H
ECAT-SO3H
procyanidin B2-SO3H
O
OH
OH
OH
OH
OH
S
O
O
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
S
O
O
OH
144. Arapitsas et al. Scientific Reports 2018
Wine Chemistry – Phenolics – Flavanols
red
sparkling
white
sparkling
white
red
ECAT-SO3H
epicatechin-SO3H
ECAT-SO3H
procyanidin B2-SO3H
O
OH
OH
OH
OH
OH
S
O
O
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
S
O
O
OH
145. Arapitsas et al. Scientific Reports 2018
Wine Chemistry – Phenolics – Flavanols
Amarone Tannat Sagrantino
6 8 10 14 16 19 24 26 31 5 6 7 14139
Age
10
Age
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
epicatechin
procyanidin B2
136 7 11 12
Age
146. Arapitsas et al. Scientific Reports 2018
Wine Chemistry – Phenolics – Flavanols
ECAT-SO3H
epicatechin-SO3H
ECAT-SO3H
procyanidin B2-SO3H
O
OH
OH
OH
OH
OH
S
O
O
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
S
O
O
OH
6 8 10 14 16 19 24 26 31 5 6 7 14139
Age
10
Age
136 7 11 12
Age
148. Arapitsas et al. Scientific Reports 2018
Wine Chemistry – Phenolics – Flavanols
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
epicatechin
procyanidin B2
ECAT-SO3H
epicatechin-SO3H
ECAT-SO3H
procyanidin B2-SO3H
O
OH
OH
OH
OH
OH
S
O
O
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
S
O
O
OH
150. Wine Chemistry – Tryptophan metabolites
OH
NH2
N
H
O
O
NH2
OH
O
OH
N
H
OH
O
OH
N
H
OH
N
H
TOL
N
OH
O
OH
N
H
O
NH O
N
H
OH
NH2
shikimic
OH
OH
OH
OOH
OOH
NH2
O
NH2
O
O
N
H
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
O
NH
N
H
O
O
O
NH2
N
H
O
epicatechin
procyanidin B2
phenylalanine
tryptophan melatoninserotonin
tryptophan ethyl ester
N-acetyl-tryptophan ethyl ester
kynurenic
anthranillic
kynurenine
indole-3-pyruvic acid
indole-3-lactic acid
indole-3-acetic acid
tryptophol
2-aminoacetophenone
OOH
NH2
anthranillic
160. Wine Metabolomics – public repositories
N
H
O
O
OH
O
OH
OH
OH
OH
http://www.ebi.ac.uk/metabolights/MTBLS137Franceschi et al. Frontiers 2014
indole-3-lactic glucoside
0
100
200
300
400
500
600
700
800
Germany Italy
area
Phoenix
Regent
162. Wine Metabolomics – public repositories
N
H
O
O
OH
O
OH
OH
OH
OH
Top 30 red grape cultivars Top 30 white grape cultivars
271 entries 181 entries
163. Wine Chemistry – Tryptophan metabolites
OH
NH2
N
H
O
O
NH2
OH
O
OH
N
H
OH
O
OH
N
H
OH
N
H
TOL
N
OH
O
OH
N
H
O
NH O
N
H
OH
NH2
shikimic
OH
OH
OH
OOH
OOH
NH2
O
NH2
O
O
N
H
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
O
OH
OH
OH
OH
OH
O
NH
N
H
O
O
O
NH2
N
H
O
epicatechin
procyanidin B2
phenylalanine
tryptophan melatoninserotonin
tryptophan ethyl ester
N-acetyl-tryptophan ethyl ester
kynurenic
anthranillic
kynurenine
indole-3-pyruvic acid
indole-3-lactic acid
indole-3-acetic acid
tryptophol
2-aminoacetophenone
OOH
NH2
anthranillic
164. Wine Chemistry – Tryptophan metabolites
O
OH
N
H S O
O OH
OH
N
H
TOL
tryptophol
red
sparkling
white
O
OH
N
H
OH
indole-3-lactic acid
O
OH
N
H
OH
S
O
O
OH
red
sparkling
white
O
OH
N
H
indole-3-acetic acid
O
OH
N
H S O
O OH
red
sparkling
white
171. OH NH
NH
O
NH2
O
S
O
O
OH
OH NH
NH
O
NH2
O
S
O
O
OH
GSSG
OH NH
NH
O
NH2
O
S
O
O
OH
S
O OH
OGSSO3H
GSSG GSSG/SO2
10/1
GSSG/SO2
1/1
GSSG/SO2
1/10
GSSG GSSG/SO2
10/1
GSSG/SO2
1/1
GSSG/SO2
1/10
Glutathione reactivity – Reactions in model wine solution
Arapitsas et al. J Chromatogr A 2016
172. OH NH
NH
O
NH2
O
S
O
O
OH
OH NH
NH
O
NH2
O
S
O
O
OH
GSSG
OH NH
NH
O
NH2
O
S
O
O
OH
S
O OH
OGSSO3H
GSSG GSSG/SO2
10/1
GSSG/SO2
1/1
GSSG/SO2
1/10
GSSG GSSG/SO2
10/1
GSSG/SO2
1/1
GSSG/SO2
1/10
Glutathione reactivity – Reactions in model wine solution
Arapitsas et al. J Chromatogr A 2016
173. OH NH
NH
O
NH2
O
SH
O
O
OH
OH NH
NH
O
NH2
O
S
O
O
OH
SO OH
O
SO2
+ H2O
HSO3
-
OH NH
NH
O
NH2
O
S
O
O
OH
OH NH
NH
O
NH2
O
S
O
O
OH
O2
Glutathione reactivity – Reactions in model wine solution
Arapitsas et al. J Chromatogr A 2016