From the journal RSC Chemical Biology Peer review history

30-Apr-2021

Dear Dr Li:

Manuscript ID: CB-REV-03-2021-000039
TITLE: Recent Developments and Applications of Quantitative Proteomics Strategies for High-Throughput Biomolecular Analyses in Cancer Research

Thank you for your submission to RSC Chemical Biology, published by the Royal Society of Chemistry. I sent your manuscript to reviewers and I have now received their reports which are copied below.

After careful evaluation of your manuscript and the reviewers’ reports, I will be pleased to accept your manuscript for publication after revisions.

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I look forward to receiving your revised manuscript.

Yours sincerely,
Professor Zaneta Nikolovska-Coleska
Associate Editor, RSC Chemical Biology

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Reviewer 1

This review describes some recent highlights and applications of using quantitative proteomics approaches in cancer research. An overview of quantiative methods is given and applications of these methods to several different cancers is highlighted. Overall, the paper is well written and does a nice job of highlighting how quantiative proteomics is being used in cancer research. The manuscript will likely be of broad interest to the field. There are several issues that I would recommend the authors address:
1) In several instances, measurements of proteins being up- and down- regulated are mentioned. Although this verbiage is common in proteomics, it is a misnomer as what is really being measured is levels of proteins, not how the proteins are regulated.
2) The paper covers a very broad topic. For an example, any individual cancer could have been the subject of an entire review, and in this case, multiple cancers are discussed. Only a few of many papers in the field are discussed. It would be helpful to explain how the highlighted papers were chosen.
3) The resolution of the figures is poor.

Reviewer 2

In the manuscript entitled ‘Recent Developments and Applications of Quantitative Proteomics Strategies for High-Throughput Biomolecular Analyses in Cancer Research’, the authors reviewed literatures on quantitative proteomics strategies, and addressed the applications of proteomic platforms into tumor biomarker discovery: biomarker discovery, validation and the transformation from bench to clinic. The manuscript was well written and summarized the recent advances and current status of proteomics in oncology. Authors provided useful information about proteomics techniques for clinicians and students in translational medicine. I would suggest that authors add a table to list important biomarkers for different tumors, which can strengthen the manuscript.

Minor points:
• Authors can replace CA19 by Carbohydrate antigen (CA) 19-9 in line 417.

Response to reviewers’ comments:

Reviewer 1

‘This review describes some recent highlights and applications of using quantitative proteomics approaches in cancer research. An overview of quantitative methods is given and applications of these methods to several different cancers is highlighted. Overall, the paper is well written and does a nice job of highlighting how quantitative proteomics is being used in cancer research. The manuscript will likely be of broad interest to the field. There are several issues that I would recommend the authors address:’

Suggestion 1: In several instances, measurements of proteins being up- and down- regulated are mentioned. Although this verbiage is common in proteomics, it is a misnomer as what is really being measured is levels of proteins, not how the proteins are regulated.

Response: We appreciate the thoughtful consideration as to whether the language presented in our manuscript is clear, concise, and allows readers to appropriately understand the breadth of unique research interests presented within the review. We present here a proteomics-centric view of quantitative cancer research and wish to frame our discussion to both agree with the field at large and to stay congruent with the original findings and discussion presented by the authors. To clarify our language and present readers with the most efficient understanding of the presented research, we have taken the reviewers’ comment and included language in our introduction that discusses our interpretation of the words “up-” and “down-regulated” (lines 61-71). This context will lend itself to readers entering the field of proteomics and will provide context to those who further pursue the referenced literature. Changes to the submission are denoted by blue text.

Suggestion 2: The paper covers a very broad topic. For an example, any individual cancer could have been the subject of an entire review, and in this case, multiple cancers are discussed. Only a few of many papers in the field are discussed. It would be helpful to explain how the highlighted papers were chosen.

Response: We thank the reviewer for the critical consideration as to the appropriateness of the literature cited within our review. We agree that the body of research is far more extensive than that which we have discussed here; certainly, providing a comprehensive review of quantitative cancer proteomics may not lend itself to the most timely, topical or helpful submission. To provide the readers with context as to how the cited literature has been chosen, we have implemented additional text that clearly states that our literature is aimed at 4 cancer types that continue to occupy large swaths of research interest, despite extensive historical focus. We also highlight the selection of references that have been published within the last 5 years (lines 76-83). The rationale for this decision is to provide readers with the most recent advances in quantitative cancer proteomics, an in-depth look as to where this research may be heading, and to provide accurate context for those seeking to begin their research. Changes to the submission are denoted by blue text.

Suggestion 3: The resolution of the figures is poor.

Response: Critical evaluation of the content presented within the manuscript is immensely appreciated. We have gone through each figure within the manuscript and provided the highest possible resolution for image. We have ensured the quality of the images is up to par with the submission of the cited authors and is in agreement with this journal’s standards and guidelines.

Reviewer 2

‘In the manuscript entitled ‘Recent Developments and Applications of Quantitative Proteomics Strategies for High-Throughput Biomolecular Analyses in Cancer Research’, the authors reviewed literatures on quantitative proteomics strategies, and addressed the applications of proteomic platforms into tumor biomarker discovery: biomarker discovery, validation and the transformation from bench to clinic. The manuscript was well written and summarized the recent advances and current status of proteomics in oncology. Authors provided useful information about proteomics techniques for clinicians and students in translational medicine. I would suggest that authors add a table to list important biomarkers for different tumors, which can strengthen the manuscript.’

Response: The authors thank the reviewer(s) for their positive feedback and encouraging support of the chosen literature. To strengthen our submission, we have incorporated the reviewer’s suggestion of summary tables so that readers may have both long- and short-form overviews of putative biomarkers for each cancer type. We have included four tables (Tables 1-4) that include details as to the protein biomarkers suggested by the original authors, the biological source/model studied in each manuscript, a brief synopsis of the authors’ findings, and citation of the original text. The tables can be found prior to the figures and are denoted with blue text.

Minor Suggestion: Authors can replace CA19 by Carbohydrate antigen (CA) 19-9 in line 417.

Response: We thank the reviewer for offering a point of clarity as we discuss this well-known cancer biomarker. We have fully incorporated this change by replacing instances of ‘CA19’ with CA19-9. This change will facilitate a stronger perception of our report and prevent obfuscation of prior knowledge.

18-May-2021

Dear Dr Li:

Manuscript ID: CB-REV-03-2021-000039.R1
TITLE: Recent Developments and Applications of Quantitative Proteomics Strategies for High-Throughput Biomolecular Analyses in Cancer Research

Thank you for submitting your revised manuscript to RSC Chemical Biology. After considering the changes you have made, I am pleased to accept your manuscript for publication in its current form. I have copied any final comments from the reviewer(s) below.

You will shortly receive a separate email from us requesting you to submit a licence to publish for your article, so that we can proceed with publication of your manuscript.

You can highlight your article and the work of your group on the back cover of RSC Chemical Biology, if you are interested in this opportunity please contact me for more information.

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Thank you for publishing with RSC Chemical Biology, a journal published by the Royal Society of Chemistry – connecting the world of science to advance chemical knowledge for a better future.

With best wishes,

Professor Zaneta Nikolovska-Coleska
Associate Editor, RSC Chemical Biology

Reviewer 1

The authors were very responsive to my comments and have addressed everything in a satisfactory manner.