Table 1

An example of using peptide ratios used to derive protein relative expression results (odorant binding protein 14 [GenBank:94158822])

Peptide


Sample

Larval ages compared

Replicate (1, 2, or 3)

1

2

3

4

5

Ln (peptide average)

Ln (protein average)


H

1, 3

1

-1.26

-1.41

-1.66

-1.82

-2.25

-1.68

-3.01

H

2

-3.29

-3.39

-3.55

-3.68

-3.74

-3.53

H

3

-3.76

-3.82

-3.82

-3.82

-3.82

-3.81

H

2, 3

1

-0.68

-0.93

-1.28

-1.32

-1.77

-1.20

-1.35

H

2

-0.85

-0.97

-1.06

-1.13

-1.62

-1.12

H

3

-1.57

-1.59

-1.69

-2.11

NA

-1.74

H

4, 3

1

3.91

3.91

3.91

3.91

NA

3.91

2.22

H

2

-0.10

0.53

0.91

1.94

3.10

1.28

H

3

0.67

1.56

1.60

1.69

1.84

1.47

H

5, 3

1

3.91

3.91

3.91

3.91

3.91

3.91

3.09

H

2

2.16

2.32

2.50

3.04

3.04

2.61

H

3

2.05

2.55

2.57

2.78

3.79

2.75

T

1, 3

1

-1.29

-1.37

-1.57

-1.80

-1.80

-1.57

-0.53

T

2

-1.68

-2.16

-2.16

NA

NA

-2.00

T

3

1.47

1.83

2.59

NA

NA

1.96

T

2, 3

1

-0.55

-0.58

-0.78

-0.91

-0.93

-0.75

-0.72

T

2

-0.34

-0.42

-0.55

-1.04

-1.42

-0.75

T

3

-0.46

-0.66

-0.86

NA

NA

-0.66

T

4, 3

1

-0.39

-0.40

-0.69

-0.70

-0.76

-0.59

-0.37

T

2

-0.06

0.24

0.38

0.70

0.81

0.41

T

3

-0.65

-0.95

-1.02

-1.07

NA

-0.92

T

5, 3

1

-0.02

-0.05

-0.27

-0.31

-0.40

-0.21

0.76

T

2

0.37

0.67

0.90

1.47

NA

0.85

T

3

0.80

1.53

1.67

2.04

2.08

1.62


Both the honey bee larval hemolymph (H) and tissue (T) samples were collected daily for 5 days post-hatching, and peptides from days 1, 2, 4, and 5 were isotopically labeled and mixed at 1:1 (by protein amount) with day 3 peptides, which were labeled differentially from the other days. Relative peptide intensities were recorded (limited at 50-fold or 3.91 in natural log (Ln)) and proteins with a minimum of 2 quantified peptides were natural log-transformed and averaged; for proteins with greater than 5 peptides, the top 5 most intense ones were selected for averaging. In samples where there were less than 5 peptides, their absence is indicated by NA (not available).

Chan and Foster Genome Biology 2008 9:R156   doi:10.1186/gb-2008-9-10-r156

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