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slide1

PCA for UPLC-MS

From this, we can see the clustering of various mutants. There is clear separation from the WT with many distinct clusters. As we can see we have distinct separations amongst the mutant population from the wild type with many clustering away from each other. The tight cluster on the right includes the lap genes, which all cluster nicely.

slide3

2000

A

A

Wild Type

A

T

V

T

V

1000

T

V

X

P

X

X

1

1

M

M

1

M

P

E

5

5

P

3

3

5

2

3

E

L

Z

E

Z

Z

W

W

0

2

G

I

W

PC2

O

D

4

L

L

D

O

4

4

G

I

G

U

O

2

Y

I

U

Y

D

Y

F

U

S

S

Q

C

S

C

R

N

Q

Q

N

R

N

R

F

C

F

B

B

B

H

H

H

-1000

K

K

K

J

J

-2000

J

-2000

-1000

0

1000

PC1

hca dendogram for uplc ms

HCA dendogram for UPLC-MS

If you will zoom out you can get a better visual. The scale is from blue (low accumulation) to red (high accumulation).

slide5

127-1-1_3

127-1-1_1

127-1-1_2

155-2-1_2

155-2-1_3

155-2-1_1

103-3-2_1

103-3-2_3

103-3-2_2

12-1-2_2

12-1-2_3

12-1-2_1

55-1-1_3

55-1-1_2

55-1-1_1

52-4-2_2

110-2-1_2

52-4-2_1

110-2-1_1

52-4-2_3

110-2-1_3

155-2-1_2

154-1-1_2

131-1-2_2

131-1-2_1

131-1-2_3

155-2-1_3

154-1-1_3

155-2-1_1

154-1-1_1

137-2-1_3

137-2-1_1

137-2-1_2

135-2-3_1

135-2-3_3

135-2-3_2

62-1-1_3

24-1-1_2

24-1-1_3

24-1-1_1

119-1-1_2

119-1-1_1

119-1-1_3

At1g33430_1

At1g33430_3

At1g33430_2

At1g65060_3

At1g65060_1

At1g65060_2

62-1-1_1

62-1-1_2

47-3-1_3

16-3-1_3

52-1-1_2

52-1-1_1

52-1-1_3

40-4-1_1

40-4-1_2

40-4-1_3

15-3-2_3

15-3-2_1

15-3-2_2

47-3-1_2

16-3-1_2

47-3-1_1

16-3-1_1

28-3-1_2

28-3-1_3

28-3-1_1

Lap4_2

Lap4_3

Lap4_1

At3g28780_1

At3g28780_3

At3g28780_2

Lap6-2_3

Lap6-2_1

Lap6-2_2

Lap5_1

Lap5_2

Lap5_3

Lap6_3

Lap6_1

Lap6_2

Lap5-6_2

Lap5-6_1

Lap5-6_3

Lap3_1

Lap3_3

Lap3_2

WT

WT

WT

4-hydroxy-3-indolylmethyl-glucosinolate_447.0528_2.4498

8-Methylsulfinyl-n-octyl glucosinolate _492.1012_3.1709

1-16:0-lysophosphatidylethanolamine_452.2789_24.1954

kaempferol 3-glucoside-7-p-coumaryl-glucoside_755.2034_3.8868

4-Methylsulfinyl-n-butyl-glucosinolate_436.039_0.6921

6-Methylsulfinyl-n-heyl-glucosinolate _464.0702_1.308

7-(methylsulfinyl)-heptyl-glucoside_478.0882_2.0476

isorhamnetin 3-glucoside-7-rhamnoside_623.1606_5.9036

1-18:3-lysophosphatidylethanolamine_474.2643_21.9428

Baicalein 7-O-glucuronide_445.0768_5.7048

Leteolin 3'-methyl ether 7-glucoside _461.1067_8.1826

kaempferol 3-glucoside-7-galacturonide_607.1662_6.8962

kaempferol-3-rhamnoside-7-rhamnoside_577.1549_6.5228

Naringenin chalcone_271.0588_10.3893

luteolin-3-7-di-O-glucosinolate_609.1452_4.8089

Kaempferol Hexose _416.1053_7.0031

Indol-3-ylmethyl-glucosinolate_447.0536_1.3604

10,16-dihydroxypalmitic acid_287.2221_14.2284

Palmitoleic acid_253.2165_29.7395

kaempferol-7-O-glucoside _447.0926_7.5553

Linolenic acid _277.2165_28.2305

Palmitic acid_255.2308_31.7811

luteolin-7-O-rhamnoside_593.1513_6.1882

Linoleic acid_279.2322_30.418

Naringenin_271.0585_9.9375

Oleic acid_281.2478_32.0921

Unknown _223.0263_14.0477

Unknown_265.1476_26.6734

Unknown_293.1778_33.0769

Unknown_321.2108_33.8278

Unknown_388.2698_12.2189

Unknown_375.2751_13.3403

Unknown_504.3098_23.7926

Unknown_344.2449_15.1693

Unknown_305.0806_13.9126

Unknown_315.1122_17.5205

Unknown_502.2924_21.4499

Unknown_504.3092_23.0687

kempferol-3-O-rutinoside _593.1503_5.555

Unknown_360.2372_8.6695

Unknown_342.229_13.0975

Unknown_476.277_23.6657

Unknown_445.077_5.0285

Unknown_480.3089_24.86

Isoscoparine_477.1029_6.9831

Unknown _881.5466_11.7747

Unknown_967.5861_11.9341

Unknown_793.4942_12.0488

Unknown_879.5295_12.1241

Unknown_749.4655_12.5328

Unknown_703.4233_12.6914

Unknown_611.3424_14.3943

Unknown_615.3735_13.0931

Unknown_595.3454_15.5652

Unknown_595.3503_15.8132

Unknown_593.3353_16.2731

Unknown_791.4764_12.379

Unknown_502.295_22.064

Robinin_739.2076_4.3732

slide6

S-plots for 4 mutants against wild type

This shows what metabolites differ from the WT and mutant. WT is differences are show in Quadrant-IV while the mutant metabolites are represented in Quadrant-II

slide8

S-Plot (WT = -1, 15-3-2 (C) = 1)

28

25

35

33

29

44

42

46

52

1.0

26

39

41

34

43

27

36

23

48

55

50

58

57

59

37

40

54

56

30

53

51

24

18

14

49

45

38

12

32

22

21

19

0.9

47

0.8

0.7

31

0.6

0.5

0.4

0.3

0.2

0.1

p(corr)[1]P (Correlation)

0.0

-0.1

-0.2

-0.3

-0.4

-0.5

20

-0.6

3

-0.7

-0.8

-0.9

7

17

1

15

5

16

13

11

10

6

4

9

8

2

-1.0

-0.0003

-0.0002

-0.0001

0.0000

0.0001

0.0002

0.0003

CoeffCS[2](Group) (X Effects)

slide9

S-Plot (WT = -1, Lap6 (I) = 1)

34

28

33

36

46

48

42

50

1.0

39

35

41

43

55

54

59

37

25

53

29

51

14

40

57

49

56

32

26

23

27

24

44

21

45

38

52

22

58

0.9

47

19

0.8

30

0.7

0.6

20

0.5

31

0.4

0.3

0.2

0.1

18

p(corr)[1]P (Correlation)

0.0

-0.1

-0.2

12

-0.3

-0.4

-0.5

-0.6

-0.7

1

3

2

7

-0.8

4

17

-0.9

15

11

8

16

5

10

6

13

9

-1.0

-0.0003

-0.0002

-0.0001

0.0000

0.0001

0.0002

0.0003

CoeffCS[2](Group) (X Effects)

slide10

S-Plot (WT = -1, 127-1-1 (J) = 1)

34

23

36

39

44

12

48

50

59

1.0

35

37

43

46

52

53

51

54

58

49

28

45

18

42

40

33

47

0.9

41

0.8

0.7

0.6

0.5

14

55

0.4

0.3

0.2

0.1

p(corr)[1]P (Correlation)

0.0

57

-0.1

-0.2

-0.3

5

29

-0.4

10

25

-0.5

-0.6

6

-0.7

26

24

30

-0.8

56

-0.9

27

31

21

38

32

1

19

2

7

22

9

8

20

11

17

4

15

13

16

3

-1.0

-0.0002

-0.0001

0.0000

0.0001

CoeffCS[2](Group) (X Effects)

slide11

S-Plot (WT = -1, 110-2-1 (V) = 1)

26

33

34

28

25

27

29

44

46

50

52

1.0

30

32

35

37

39

43

12

48

58

19

24

41

42

14

51

18

49

40

59

45

38

47

20

0.9

31

0.8

0.7

7

0.6

0.5

0.4

54

17

0.3

0.2

0.1

p(corr)[1]P (Correlation)

0.0

-0.1

-0.2

-0.3

-0.4

23

-0.5

10

5

-0.6

9

22

-0.7

36

21

-0.8

13

-0.9

16

53

56

55

57

2

11

1

6

8

4

15

3

-1.0

-0.0003

-0.0002

-0.0001

0.0000

0.0001

0.0002

CoeffCS[2](Group) (X Effects)