Reviewer's report
Title:Comparative proteomics study on liver mitochondria of primary biliary
cirrhosis mouse model
Version: 3Date:8 November 2012
Reviewer: Jeffrey T.-J. Huang
Reviewer's report:
Dear Editor,
The manuscript by Li et al described a comparative mitochondrial proteomic
study in primary biliary cirrhosis mouse model. This is an interesting study,
particularly the time dependent changes in the 17b-HSD8, ECHDC2, ADH levels
in the mouse model. A few major points and minor points are listed below, which
I hope will help improve the quality of this manuscript.
Major Compulsory Revisions
1. From figure 2, it seems that only a pair of pooled sample from each group was
compared and there was no technical replication done on the same experiment.
This issue was addressed partially with the Western blot data in Figure 4.
However, for those which were not validated, there is some uncertainty. A
statement of this limitation should be included.
2. Page 6, authors state that “…only fold changes >1.4 or <0.72.” will be
considered significant. Justification is required to provide a basis for this as there
is no statistics behind these thresholds.
3. The description needs to be better referenced (and perhaps more conserved
in the interpretation as in some cases there is no direct data in this study to
support it). A couple of examples,
a. authors suggest the up-regulation of the 11 proteins in oxidation/reduction as
an indication of oxidative stress but it would be just reflecting a higher demand of
energy by the inflammatory cells. References are also required to support the
oxidative stress hypothesis.
b. Page 12, authors suggest the up-regulation of 17b-HSD8 can lead to a
decrease of estrogen concentration, which might result in the destruction of bile
ducts etc. Data from the histology of these samples will be very useful to support
this claim (together with a ref).
Minor Essential Revisions
4. The individual peptide signals of proteins listed in Table 1 and 2 needs to be
listed in a supplementary data.
5. The false discovery rate of protein identification (at peptide and protein levels)
should be stated (page 6).
6. Figure 4A, Control and model figures are not aligned with the table on the left.
Also, the reason of using ATPb as a loading control in Figure 4 should be
explained.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests.
Reviewer's report
Title:Comparative proteomics study on liver mitochondria of primary biliary
cirrhosis mouse model
Version: 3Date:8 November 2012
Reviewer: Jeffrey T.-J. Huang
Reviewer's report:
Dear Editor,
The manuscript by Li et al described a comparative mitochondrial proteomic
study in primary biliary cirrhosis mouse model. This is an interesting study,
particularly the time dependent changes in the 17b-HSD8, ECHDC2, ADH levels
in the mouse model. A few major points and minor points are listed below, which
I hope will help improve the quality of this manuscript.
Major Compulsory Revisions
1. From figure 2, it seems that only a pair of pooled sample from each group was
compared and there was no technical replication done on the same experiment.
This issue was addressed partially with the Western blot data in Figure 4.
However, for those which were not validated, there is some uncertainty. A
statement of this limitation should be included.
2. Page 6, authors state that “…only fold changes >1.4 or <0.72.” will be
considered significant. Justification is required to provide a basis for this as there
is no statistics behind these thresholds.
3. The description needs to be better referenced (and perhaps more conserved
in the interpretation as in some cases there is no direct data in this study to
support it). A couple of examples,
a. authors suggest the up-regulation of the 11 proteins in oxidation/reduction as
an indication of oxidative stress but it would be just reflecting a higher demand of
energy by the inflammatory cells. References are also required to support the
oxidative stress hypothesis.
b. Page 12, authors suggest the up-regulation of 17b-HSD8 can lead to a
decrease of estrogen concentration, which might result in the destruction of bile
ducts etc. Data from the histology of these samples will be very useful to support
this claim (together with a ref).
Minor Essential Revisions
4. The individual peptide signals of proteins listed in Table 1 and 2 needs to be
listed in a supplementary data.
5. The false discovery rate of protein identification (at peptide and protein levels)
should be stated (page 6).
6. Figure 4A, Control and model figures are not aligned with the table on the left.
Also, the reason of using ATPb as a loading control in Figure 4 should be
explained.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests.
Please review this paper.
user
Reviewer's report
Title:Comparative proteomics study on liver mitochondria of primary biliary
cirrhosis mouse model
Version: 3Date:8 November 2012
Reviewer: Jeffrey T.-J. Huang
Reviewer's report:
Dear Editor,
The manuscript by Li et al described a comparative mitochondrial proteomic
study in primary biliary cirrhosis mouse model. This is an interesting study,
particularly the time dependent changes in the 17b-HSD8, ECHDC2, ADH levels
in the mouse model. A few major points and minor points are listed below, which
I hope will help improve the quality of this manuscript.
Major Compulsory Revisions
1. From figure 2, it seems that only a pair of pooled sample from each group was
compared and there was no technical replication done on the same experiment.
This issue was addressed partially with the Western blot data in Figure 4.
However, for those which were not validated, there is some uncertainty. A
statement of this limitation should be included.
2. Page 6, authors state that “…only fold changes >1.4 or <0.72.” will be
considered significant. Justification is required to provide a basis for this as there
is no statistics behind these thresholds.
3. The description needs to be better referenced (and perhaps more conserved
in the interpretation as in some cases there is no direct data in this study to
support it). A couple of examples,
a. authors suggest the up-regulation of the 11 proteins in oxidation/reduction as
an indication of oxidative stress but it would be just reflecting a higher demand of
energy by the inflammatory cells. References are also required to support the
oxidative stress hypothesis.
b. Page 12, authors suggest the up-regulation of 17b-HSD8 can lead to a
decrease of estrogen concentration, which might result in the destruction of bile
ducts etc. Data from the histology of these samples will be very useful to support
this claim (together with a ref).
Minor Essential Revisions
4. The individual peptide signals of proteins listed in Table 1 and 2 needs to be
listed in a supplementary data.
5. The false discovery rate of protein identification (at peptide and protein levels)
should be stated (page 6).
6. Figure 4A, Control and model figures are not aligned with the table on the left.
Also, the reason of using ATPb as a loading control in Figure 4 should be
explained.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Needs some language corrections before being
published
Statistical review: Yes, but I do not feel adequately qualified to assess the
statistics.
Declaration of competing interests:
I declare that I have no competing interests.
assistant