Reviewer's report
Title:Comparative analysis of inflamed and non-inflamed colon biopsies reveals
strong proteomic inflammation profile in patients with ulcerative colitis
Version: 1Date:23 March 2012
Reviewer: Grainne Lennon
Reviewer's report:
- Major Compulsory Revisions
1. Reproducabiltiy of 2D gels: The authors made no reference in the methods or
text of the document regarding the reproducibility of the 2D gels and analysis.
Were technical repeats of the gels and analysis carried out and if so what was
the level of reproducibility between the reps.
2: Validation of protein expressions: The authors made no reference in the
methods or text of the document regarding the validation of the protein
expression profiles. It is worth considering the implementation of a validation
experiment such as immunoblotting for specific proteins or
immunohistochemistroy assays on the histological blocks. This would lend further
support to the authenticity of the results and methods.
- Minor Essential Revisions (Minor issues not for publication)
1: Abstract , Paragraph 1: Change “wanted” to “aimed”.
1. Abstract, Paragraph 3: The authors state 44 individual protein spots were
identified. Later in the document (Background, Paragraph 6, Results, Paragraph
9) the authors state 33 unique proteins were identified. The authors need to
clarify if firstly these proteins are unique rather than individual, and if so change
this to the correct number. If the authors are stating that in total 44 proteins were
identified then perhaps more value would be added to the abstract by discussing
the proteins which are unique and can act as candidate markers for UC rather
than discussing proteins which were simply identified.
2. Abstract, Paragraph 4: The authors state that the proteins have been identified
as candidate markers for disease severity. This comment needs to be changed
as these markers have not been directly correlated to disease severity/activity
(eg. Disease scoring indices). These proteins have been correlated to UC
disease only.
3. Background, Paragraph 6: See comment 2 above.
4. Methods, Paragraph 1: The authors should give information regarding the
Healthy Controls and why these individuals were undergoing endoscope
procedures.
5. Methods, Paragraph 1: The authors state the treatments each of the 20 UC
patients were receiving at the time of sampling. The number of patients
described total 25. This needs to be clarified.
6. Methods, Paragraph 5: The authors should be more specific in terms of what
criteria were manually defined e.g. sensitivity, min peak values, min and max size
scale etc.
7. Results, Figures 2 &3: The size and resolution of these images are small
making the referenced data points hard to see. Can the quality of these images
be improved?
9. Results, Paragraph 8: See comment 3 above.
10. Results, Tables 1: insert a full stop at the end of the table legend
11. References Number 21: Typing error in the title of the reference
“Genome-wide”.
- Discretionary Revisions
1. The authors should consider inserting a table listing the 33 identified proteins
which are unique in their expression to UC patients.
2. It is worth commenting in the text of the discussion regarding the clinical
reasons the healthy controls were undergoing endoscopes. The authors do state
that the healthy controls were not patients with colorectal carcinoma, however if
these individuals were undergoing endoscoping for reasons such a polyp
screening then this should be acknowledged. As stated in the introductions some
inflammatory markers can be increased in polyps.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Reviewer's report
Title:Comparative analysis of inflamed and non-inflamed colon biopsies reveals
strong proteomic inflammation profile in patients with ulcerative colitis
Version: 1Date:23 March 2012
Reviewer: Grainne Lennon
Reviewer's report:
- Major Compulsory Revisions
1. Reproducabiltiy of 2D gels: The authors made no reference in the methods or
text of the document regarding the reproducibility of the 2D gels and analysis.
Were technical repeats of the gels and analysis carried out and if so what was
the level of reproducibility between the reps.
2: Validation of protein expressions: The authors made no reference in the
methods or text of the document regarding the validation of the protein
expression profiles. It is worth considering the implementation of a validation
experiment such as immunoblotting for specific proteins or
immunohistochemistroy assays on the histological blocks. This would lend further
support to the authenticity of the results and methods.
- Minor Essential Revisions (Minor issues not for publication)
1: Abstract , Paragraph 1: Change “wanted” to “aimed”.
1. Abstract, Paragraph 3: The authors state 44 individual protein spots were
identified. Later in the document (Background, Paragraph 6, Results, Paragraph
9) the authors state 33 unique proteins were identified. The authors need to
clarify if firstly these proteins are unique rather than individual, and if so change
this to the correct number. If the authors are stating that in total 44 proteins were
identified then perhaps more value would be added to the abstract by discussing
the proteins which are unique and can act as candidate markers for UC rather
than discussing proteins which were simply identified.
2. Abstract, Paragraph 4: The authors state that the proteins have been identified
as candidate markers for disease severity. This comment needs to be changed
as these markers have not been directly correlated to disease severity/activity
(eg. Disease scoring indices). These proteins have been correlated to UC
disease only.
3. Background, Paragraph 6: See comment 2 above.
4. Methods, Paragraph 1: The authors should give information regarding the
Healthy Controls and why these individuals were undergoing endoscope
procedures.
5. Methods, Paragraph 1: The authors state the treatments each of the 20 UC
patients were receiving at the time of sampling. The number of patients
described total 25. This needs to be clarified.
6. Methods, Paragraph 5: The authors should be more specific in terms of what
criteria were manually defined e.g. sensitivity, min peak values, min and max size
scale etc.
7. Results, Figures 2 &3: The size and resolution of these images are small
making the referenced data points hard to see. Can the quality of these images
be improved?
9. Results, Paragraph 8: See comment 3 above.
10. Results, Tables 1: insert a full stop at the end of the table legend
11. References Number 21: Typing error in the title of the reference
“Genome-wide”.
- Discretionary Revisions
1. The authors should consider inserting a table listing the 33 identified proteins
which are unique in their expression to UC patients.
2. It is worth commenting in the text of the discussion regarding the clinical
reasons the healthy controls were undergoing endoscopes. The authors do state
that the healthy controls were not patients with colorectal carcinoma, however if
these individuals were undergoing endoscoping for reasons such a polyp
screening then this should be acknowledged. As stated in the introductions some
inflammatory markers can be increased in polyps.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
Please review this paper.
user
Reviewer's report
Title:Comparative analysis of inflamed and non-inflamed colon biopsies reveals
strong proteomic inflammation profile in patients with ulcerative colitis
Version: 1Date:23 March 2012
Reviewer: Grainne Lennon
Reviewer's report:
- Major Compulsory Revisions
1. Reproducabiltiy of 2D gels: The authors made no reference in the methods or
text of the document regarding the reproducibility of the 2D gels and analysis.
Were technical repeats of the gels and analysis carried out and if so what was
the level of reproducibility between the reps.
2: Validation of protein expressions: The authors made no reference in the
methods or text of the document regarding the validation of the protein
expression profiles. It is worth considering the implementation of a validation
experiment such as immunoblotting for specific proteins or
immunohistochemistroy assays on the histological blocks. This would lend further
support to the authenticity of the results and methods.
- Minor Essential Revisions (Minor issues not for publication)
1: Abstract , Paragraph 1: Change “wanted” to “aimed”.
1. Abstract, Paragraph 3: The authors state 44 individual protein spots were
identified. Later in the document (Background, Paragraph 6, Results, Paragraph
9) the authors state 33 unique proteins were identified. The authors need to
clarify if firstly these proteins are unique rather than individual, and if so change
this to the correct number. If the authors are stating that in total 44 proteins were
identified then perhaps more value would be added to the abstract by discussing
the proteins which are unique and can act as candidate markers for UC rather
than discussing proteins which were simply identified.
2. Abstract, Paragraph 4: The authors state that the proteins have been identified
as candidate markers for disease severity. This comment needs to be changed
as these markers have not been directly correlated to disease severity/activity
(eg. Disease scoring indices). These proteins have been correlated to UC
disease only.
3. Background, Paragraph 6: See comment 2 above.
4. Methods, Paragraph 1: The authors should give information regarding the
Healthy Controls and why these individuals were undergoing endoscope
procedures.
5. Methods, Paragraph 1: The authors state the treatments each of the 20 UC
patients were receiving at the time of sampling. The number of patients
described total 25. This needs to be clarified.
6. Methods, Paragraph 5: The authors should be more specific in terms of what
criteria were manually defined e.g. sensitivity, min peak values, min and max size
scale etc.
7. Results, Figures 2 &3: The size and resolution of these images are small
making the referenced data points hard to see. Can the quality of these images
be improved?
9. Results, Paragraph 8: See comment 3 above.
10. Results, Tables 1: insert a full stop at the end of the table legend
11. References Number 21: Typing error in the title of the reference
“Genome-wide”.
- Discretionary Revisions
1. The authors should consider inserting a table listing the 33 identified proteins
which are unique in their expression to UC patients.
2. It is worth commenting in the text of the discussion regarding the clinical
reasons the healthy controls were undergoing endoscopes. The authors do state
that the healthy controls were not patients with colorectal carcinoma, however if
these individuals were undergoing endoscoping for reasons such a polyp
screening then this should be acknowledged. As stated in the introductions some
inflammatory markers can be increased in polyps.
Level of interest: An article whose findings are important to those with closely
related research interests
Quality of written English: Acceptable
Statistical review: No, the manuscript does not need to be seen by a
statistician.
Declaration of competing interests:
I declare that I have no competing interests.
assistant