High-1

Change of the ratio ((X/Y))

-12 -10 -8 -6 -4 -2 0 2

Cou

nt

0

20

40

60

80

100

High-2

Change of the ratio ((X/Y))

-2.0 -1.5 -1.0 -0.5 0.0 0.5 1.0 1.5

Cou

nt

0

20

40

60

80

100

120

140

160

180

Low-1

Change of the ratio ((X/Y))

-10 -8 -6 -4 -2 0 2 4

Cou

nt

0

20

40

60

80

100

120

140

Low-2

Change of the ratio (X/Y))

-4 -3 -2 -1 0 1

Cou

nt

0

20

40

60

80

100

120

140

Figure S1.

Histogram of the scalar relative amount between replicates (SRA[rep, k]). Each graph contains the

accumulated results of the total proteins in the comparison between replicates. Zero indicates the

same quantity (1.0 fold) and red line represents a simulation of the Normal/Gaussian distribution.

RTS

1.0 1.2 1.4 1.6 1.8

Ave

rage

rela

tive

amou

nt o

f int

erna

l sta

ndar

ds(A

ve_S

RA[r

ep, I

Nj

])

1.0

1.1

1.2

1.3

1.4

1.5

1.6

Figure S2.

The correlation of the average relative amount of internal standards between replicates and RTS. No

linear correlation was observed (r2=0.486).

Group 4 (HR279-3)

Log (NSAF)

0.01 0.1 1 10

Log(N

SAF)

0.01

0.1

1

10

A/B: 0.912A/C: 0.908B/C: 0.945

Group 3 (HR270-1)

Log (NSAF)

0.01 0.1 1 10

Log(N

SAF)

0.01

0.1

1

10

A/B: 0.921A/C: 0.890B/C: 0.867

Group 2 (JHK24-3)

Log (NSAF)

0.01 0.1 1 10

Log(N

SAF)

0.01

0.1

1

10

A/B: 0.916A/C: 0.964B/C: 0.958

Group 1 (JHK24-1)

Log (NSAF)

0.01 0.1 1 10

Log(N

SAF)

0.01

0.1

1

10

A/B: 0.922A/C: 0.859B/C: 0.892

High-1 High-2

Low-1 Low-2

Figure S3

The log-log plate of NSAF of total proteins between replicates. The comparison between replicates

A/B, B/C and A/C are represented as circle, reverse triangle and square, respectively. The linear

regression coefficient of each comparison is listed next to the symbol in parenthesis.

Figure S4

Linear correlation between SD_SRA[rep, INI] and the RTS values. Mass spectrometric data were

retrieved from the ProteomeXchange website. Escherichia coli whole cell proteome of six replicates

were compared for their reproducibility. The expression of protein were determined by the GPM

machine with the FDR less than 0.75%. Protein identification within six replicates were determined

by the algorithm described in the Materials and Methods. Since the number of replicates were six in

this dataset, the score (ID_S(Pk)) 6 were considered present in the sample. ≧