figure s1. histogram of the scalar relative amount between replicates (sra[rep, k]). each graph...
TRANSCRIPT
High-1
Change of the ratio ((X/Y))
-12 -10 -8 -6 -4 -2 0 2
Cou
nt
0
20
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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
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Low-1
Change of the ratio ((X/Y))
-10 -8 -6 -4 -2 0 2 4
Cou
nt
0
20
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120
140
Low-2
Change of the ratio (X/Y))
-4 -3 -2 -1 0 1
Cou
nt
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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. ≧