-1200 -1100 -1000 -900 -800 -700 -600 -500 -400 -300 -200 -100 0 100 200 300 400 500 600 700 800 900 1000 1100 1200 -600 -500 -400 -300 -200 -100 0 100 200 300 400 500 600 t[ 1 ] t[4]
Scores Comp[4] vs. Comp[1] colored by Variety
Chardonnay Grillo Inzolia Muller Pinot grigio QC Traminer Hotelling’s T2 Ellipse (95%) = (559.1; 1139) R2X[4] = 0.06998 R2X[1] = 0.2906
EZinf o 2 - nomacorc2_1QC (M3: PCA-X) - 2015-01-23 12: 22:22 (UTC+1)
3 x Grillo
5 x Pinot gris
1 x Inzolia
1 x Muller Thurgau
1 x Chardonnay
1 x Traminer
6 x varieties
12 x wines
N
2O
22 x bottling conditions
(4+4)x12 = 96 bottles (+)
~8000 features
statistical noise
QC
LC-MS Wine Metabolomics:
workflow
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation Method adaptation MetaDB PCA QC samples OPLS-DAXCMS Metadata Visual control TargetLynx Statistics Targeted analysis Internal database External database MS/MS Randomi-zationLC-MS Wine Metabolomics:
method
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation Method adaptationLC-MS Wine Metabolomics:
markers
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation XCMS OPLS-DA Visual control TargetLynx Statistics Targeted analysisfalse positives
false negatives
(tentative) bio-markers
LC-MS Wine Metabolomics:
markers
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation Visual control TargetLynx Statistics1.
Check chromatogram
2.
Check MS spectra
3.
Peak integration
4.
QC variability Vs. p-values
C
T
QC
C
T
QC
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation
External databases
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
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation
The great unknown
LC-MS Wine Metabolomics:
Hypothesis
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generationO
O
H
OH
O
O
H
O
H
O
O
O
O
O
H
O
H
O
2
N
2O
2LC-MS Wine Metabolomics:
Hypothesis
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generationglutathione
O
2O
H
NH
NH
O
NH
2
O
S
O
O
O
H
O
H
NH
NH
O
NH
2
O
S
O
O
O
H
O
H
NH
NH
O
NH
2
O
SH
O
O
O
H
N
2O
2Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation
O
2, HSO
3-O
H
NH
NH
O
NH
2
O
SH
O
O
O
H
O
H
NH
NH
O
NH
2
O
S
O
O
O
H
S
O
OH
O
LC-MS Wine Metabolomics:
Hypothesis
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation
LC-MS Wine Metabolomics:
Message
O H NH NH O NH2 O SH O O O H O H NH NH O NH2 O S O O O H S O OH O SO2 + H2O HSO3 -O H NH NH O NH2 O S O O O H O H NH NH O NH2 O S O O O H
O
2LC-MS Wine Metabolomics:
Annotation
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generationLow O
2LC-MS Wine Metabolomics:
Annotation
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation m/z 120 140 160 180 200 220 240 260 280 300 320 340 360 380 % 0 100D006_Pinot_RP_neg 21 (14.263) Cm (17:32) 18: TOF MSMS 366.12ES-
765 142.0669 765 128.0501 35 204.0672 216 186.0524 148 143.0557 132 159.0161 20 205.0008 24 270.8094 19 247.8298 13 287.8287 17 366.1111 8 329.5197 2
MS/MS
N H OH O OH162
hexose
N
H
O
O
OH
O
OH
OH
O
H
OH
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation
N
H
O
O
OH
O
OH
OH
O
H
OH
S
O
OH
O
O
2, HSO
3-High O
2Low O
2N
H
O
O
OH
O
OH
OH
O
H
OH
LC-MS Wine Metabolomics:
Annotation
Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation
O
NH
NH
O
OH
O
H
S
S
O
O
OH
O
NH
NH
O
OH
O
H
SH
N
H
OH
S
O
O
OH
N
H
OH
O
2, HSO
3-
O
2, HSO
3-O
NH
2S
OH
S
O
O
O
H
O
NH
2S
H
OH
O
2, HSO
3Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation
LO: Low O
2HO: High O
2Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation
O
OH
OH
O
H
OH
OH
O
OH
OH
O
H
OH
OH
O
OH
OH
O
H
OH
OH
O
OH
OH
O
H
OH
OH
S
O
O
O
-O
2, HSO
3Experimental design Experiment LC-MS analysis Quality Control Markers detection Markers validation Markers identification Hypothesis generation
http://www.ebi.ac.uk/metabolights/MTBLS137
Franceschi et al. Frontiers 2014
indole-3-lactic glucoside
0 100 200 300 400 500 600 700 800Germ any Italy
a re a Phoenix Re gent
