02101620468121418 retention time (min) relative intensity leaf esi (+) esi () supplementary figure 1...
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0 2 10 16 204 6 8 12 14 18
Retention time (min)
Rel
ativ
e in
ten
sity
LeafESI (+)ESI (−)
Supplementary Figure 1 Total ion current chromatogram of lipids from rice leaves.
Supplementary Figure 1
PC
PI
PE
DGDGPG
SQDG
GlcCer
MGDG
SG
Supplementary Figure 2. Structural characterization of triterpenoid saponins. (A) Positive MS/MS of tomatine, and (B) avenancin A-1 are displayed. The m/z values of precursor ions are shown in parentheses. Gal, galactose; Glc, glucose; Xyl, xylose; Ara, arabinose; N-MeAnth, N-methylanthranilic acid.
A
Rel
ativ
e I
nte
nsi
ty (
%)
B
Rel
ativ
e I
nte
nsi
ty (
%)
300 500 600 800 900 1000 1100700400
m/z
m/z
100
75
50
25
0
100
75
50
25
0
m/z 638.404
m/z 932.496m/z 469.330m/z 770.439m/z 451.319
m/z 423.319
Glc(⊿162)
Glc(⊿162)
Ara(⊿132)
N-MeAnth(⊿151)
(m/z 1094.549)
(m/z 1034.535)
300 500 600 800 900 1000 1100700400
Glc(⊿162)
Xyl(⊿132)
Glc(⊿162)
Gal(⊿162)
m/z 578.403
m/z 416.353
m/z 902.515m/z 740.458
Supplementary Figure 2
Supplementary Figure 3
Supplementary Figure 3 TGDG in tgd3 mutant.(A) Positive MS of TGDG in tgd3 mutant (tR 12.5 min). (B) Analysis of 34:6 TGDG in the wild type and tgd3 mutant. The intensity of extracted ion chromatogram of [M+NH4]+ of 34:6 TGDG in the tgd3 is set as 100%. The baseline is shifted for convenience.(C) Heat map expression of profiles of molecular-related ions of TGDG in wild type and tgd3 mutant. Each colored bar within a column represents an ion detected by positive LC-MS in the crude lipid extracts of the wild type and tgd3 mutants (biological replicates = 4). Peak picking and alignments were performed using Shimadzu Profiling Solution software (tolerance for m/z variation, 20 mDa; noise level, 2e5; tolerance for tRvariation, 0.1 min). Deisotope and deconvolution procedures were omitte. Peak intensities were normalized based on [M+H]+ of internal standard. The color of each bar represents the z-scored intensity of the ions of the corresponding lipid species.
m/z 1089.678, [M+NH4+1]+ of 34:6 TGDGm/z 1093.634, [M+Na]+ of 34:6 TGDGm/z 1088.671, [M+NH4]+ of 34:6 TGDG
Col-0 tgd3
-2.9 1.0 2.9
0 2 10 16 204 6 8 12 14 18
Retention time (min)
Rel
ativ
e in
ten
sity
tgd3
WT
B
34:6 TGDG
A
Rel
ativ
e I
nte
nsi
ty (
%)
m/z
100
75
50
25
0
m/z 1088.677, [M+NH4]+ of 34:6 TGDG
m/z 1109.600,[M+K]+ of 34:6 TGDG
m/z 1093.628, [M+Na]+ of 34:6 TGDG
C
900 950 1000 1050 1100 1150 1200 1250
not detected
Supplementary Figure 4. Structural characterization of two types of 34:6 DGDG (A) Negative MS/MS of 34:6 Gal(1→6)GalDG and (B) 34:6 Gal(1→6)GalDG are displayed. The m/z values of precursor ions are shown in parentheses
m/z
A
Rel
ativ
e I
nte
nsi
ty (
%)
100
75
50
25
0300 400 600 700 1000500
2×Gal–2×H2O
(⊿324)
800 900
m/z 907.520, [M–H]–m/z 629.312
m/z
B
Rel
ativ
e I
nte
nsi
ty (
%)
100
75
50
25
0300 400 600 700 1000500
2×Gal–2×H2O
(⊿324)
800 900
m/z 907.521, [M–H]–
m/z 629.314
(m/z 953.5, [M+HCO2]– )
(m/z 953.5, [M+HCO2]– )
Supplementary Figure 4
Supplementary Figure 5. OPLS-DA of lipidome data of ats1-1 and wild type. (A) Score scatter plot (R2Y=0.996, Q2=0.990, R2X=0.698). The confidence intervals correspond to the 2 or 3 sigma limits, i.e., 2 or 3 standard deviations of the vectors is displayed. (B) S-plot. The variables that changed most and have a strong contribution for class separation are circled. Details of variables circled in upper right and lower left are shown in Supplementary Tables 2 and 3.
B
-40
-30
-20
-10
0
10
20
30
40
1 2 3 4 5 6 7 8
Num
2 SD
2 SD
3 SD
3 SD
fad6-1
Col-0Pre
d.
Com
p. 1
A
Supplementary Figure 5
0.1 0.20-0.3 -0.1-0.2
0.0
0.2
0.4
0.6
0.8
1.0
-0.2
-0.4
-0.6
-0.8
-1.0
p(c
orr)
w[1]P
Supplementary Table 2
Supplementary Table 3
Supplementary Figure 6
Supplementary Figure 6. OPLS-DA of lipidome data of ats1-1 and wild type. (A) Score scatter plot (R2Y=0.990, Q2=0.985, R2X=0.736). The confidence intervals correspond to the 2 or 3 sigma limits, i.e., 2 or 3 standard deviations of the vectors is displayed. (B) S-plot. The variables that changed most and have a strong contribution for class separation are circled. Details of variables circled in upper right and lower left are shown in Supplementary Tables 4 and 5.
10 200-0.3 -0.1-0.2
B
-40
-30
-20
-10
0
10
20
30
40
1 2 3 4 5 6 7 8
Num
2 SD
2 SD
3 SD
3 SD
fad7-2
Col-0Pre
d.
Com
p. 1
A
0.0
0.2
0.4
0.6
0.8
1.0
-0.2
-0.4
-0.6
-0.8
-1.0
p(c
orr)
w[1]P
Supplementary Table 4
Supplementary Table 5