Plant Metabolomics: Current Initiatives and Future Prospects

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

The authors submitted an interesting review type paper which deals with plant metabolites, their analysis and possible function in the organism. Since the understanding of plant metabolites can improve various crop or bioactive substances productions, the manuscript topic is important and timely.

The authors summarise many aspects of metabolomics especially metabolites databases and data analyses. The metabolomic employment in crop production and investigation of plant stress physiology, assessing of nutrients or plant-microorganisms interactions is clarified.

The structure of the text and the manuscript design are logic. Reader can read the paper easily. Furthermore, the authors cite relevant and the most important references. In general view, the paper is well-written.

Author Response

Thank you for your valuable comments.

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript titled "Plant Metabolomics: Current Initiatives and Future Prospects" provides a comprehensive and well-structured overview of the existing literature in the field of plant metabolomics. The authors have displayed a strong command of the subject matter and have adeptly organized the content. However, due to its resemblance to other published reviews in this area, I recommend major revisions to enhance its originality and contribution.

 

1. Although the review is extensive, it appears to share similarities with other published reviews in the field. To set this manuscript apart, the authors should emphasize original insights, unique viewpoints, or critical analysis. It is crucial to identify and highlight gaps in the existing literature.

 

2. The review would benefit from delving deeper into specific aspects of the subject matter. Exploring different angles or methodologies, such as the application of artificial intelligence (AI) in plant metabolomics, which is a relatively new field, is encouraged.

 

3. A thorough examination of citations and references is necessary. The authors should ensure the inclusion of the most recent and high-impact studies, while also providing proper context for the selected sources. Additionally, they should discuss some of the latest and most influential plant metabolomics review papers, highlighting the originality and contribution of this review.

 

4. The figures presented in the manuscript are quite conventional and resemble those found in other reviews in the field. It is recommended to include figures and tables that are unique to this review, ones that go beyond standard introductory illustrations commonly found in a Google search.

 

In summary, this review article is well-crafted and serves as a valuable resource for researchers and readers interested in plant metabolomics. To enhance its distinctiveness and significance among other reviews, I recommend the revisions as outlined above. The manuscript holds great promise and has the potential to make a substantial contribution to the field once the recommended revisions are incorporated.

Comments on the Quality of English Language

The English in this review article maintains a commendable level of clarity and readability.

Author Response

Reviewer 2
1	The manuscript titled "Plant Metabolomics: Current Initiatives and Future Prospects" provides a comprehensive and well-structured overview of the existing literature in the field of plant metabolomics. The authors have displayed a strong command of the subject matter and have adeptly organized the content. However, due to its resemblance to other published reviews in this area, I recommend major revisions to enhance its originality and contribution.	Thank you for the comments. As per the reviewers comments we have revised the manuscript.
2	Although the review is extensive, it appears to share similarities with other published reviews in the field. To set this manuscript apart, the authors should emphasize original insights, unique viewpoints, or critical analysis. It is crucial to identify and highlight gaps in the existing literature.	Manuscript was improved as per reviewer suggestion.
3	The review would benefit from delving deeper into specific aspects of the subject matter. Exploring different angles or methodologies, such as the application of artificial intelligence (AI) in plant metabolomics, which is a relatively new field, is encouraged.	We thank the reviewer for the critical comments. In the revised manuscript we have included the application of artificial intelligence (AI) in plant metabolomics.
4	A thorough examination of citations and references is necessary. The authors should ensure the inclusion of the most recent and high-impact studies, while also providing proper context for the selected sources. Additionally, they should discuss some of the latest and most influential plant metabolomics review papers, highlighting the originality and contribution of this review.	As per the reviewers comments we have revised the manuscript
5	The figures presented in the manuscript are quite conventional and resemble those found in other reviews in the field. It is recommended to include figures and tables that are unique to this review, ones that go beyond standard introductory illustrations commonly found in a Google search.	Thank you for the comments. The figures mentioned in the manuscript were originally customized by the authors according to the content of the review and in addition, Figure 3 on Application of machine learning in Plant metabolomics is included.
6	In summary, this review article is well-crafted and serves as a valuable resource for researchers and readers interested in plant metabolomics. To enhance its distinctiveness and significance among other reviews, I recommend the revisions as outlined above. The manuscript holds great promise and has the potential to make a substantial contribution to the field once the recommended revisions are incorporated.	Thank you for the comments. As per the reviewers comments we have revised the manuscript.

Reviewer 3 Report

Comments and Suggestions for Authors

Manuscript number: cimb-2674190

Manuscript title: Plant Metabolomics: Current Initiatives and Future Prospects  

Authors: Sudha Manickam, Veera Ranjani Rajagopalan, Rohit Kambale, Raghu Rajsekaran, Selvaraju Kanagarajan, and Raveendran Muthurajan 

The topic treated in the present manuscript is of potential interest for the Journal readership, and may be useful as a general overview on recent advances about metabolomics in plants.

Before an acceptable standard for publication is reached, however, a number of points require adequate consideration on the part of the Authors. 

1)      First of all, about the use of English: I warmly recommend the Authors to have their manuscript thoroughly checked by a colleague of theirs having ample familiarity with written scientific English. Even better, by a professional editing service. It is not at all a matter of pure style, here, but rather of clarity (e.g. lines 186-188, 202-205, 291-301, and so forth)

2)      The second point is about editing, which is rather poor, at times. Typos (e.g. lines 55, 99-100, 137, 262, 389, and so forth) truncated or incomplete sentences (e.g. lines 132, 172-173, 248-249, 283, and so forth) are rather frequent in the present manuscript

3)      I cannot agree with the concept expressed at lines 52-53, because plants diseases are of course just one of the innumerable fields in which metabolomics can assist plant physiologists

4)      I have a curiosity about the paragraph dealing with metabolomics and drug investigation (lines 212-235) …Which is the link among drugs and plants, in the present context? Would the Authors clarify/explain/demonstrate?

5)      I was unable to understand the concept appearing at lines 361-362…In which sense the metabolome is “smaller” than proteome and genome?....Indeed, the logic, as well as the actual biology, could suggest that exactly the contrary is true…Do the 25,000-40,000 variants of a single class of plant “secondary” metabolites, such as terpenoids, thought to be present across the plant kingdom, are to be regarded as a small number? 

6)      I would like the Authors to clarify about the differences among the “targeted/untargeted” approaches (e.g. line 75), just to the benefit of the many readers who might be not familiar with those terms/concepts.

7)      About the use of uncommon acronyms, e.g. CE (line75), PGPB (line 340), and so forth, which should be defined in full, upon their first mention in the text

8)      About the compulsive use of the generic terms “etc” (e.g lines 45, 86, and so forth) which should be always avoided, in any scientific manuscript, because it inspires inaccuracy, incompleteness  and hastiness

9)      About the compulsive use of capital letters as the first letters, even in words which do not require them (e.g. the names of metabolites, lines 167, 180, and so forth)

All the above considering, I recommend major revision of the present manuscript, properly and carefully addressing all the points raised above.

Comments on the Quality of English Language

Extensive editing of English language required

Author Response

S. No	Comments	Replies
Reviewer 3
1	First of all, about the use of English: I warmly recommend the Authors to have their manuscript thoroughly checked by a colleague of theirs having ample familiarity with written scientific English. Even better, by a professional editing service. It is not at all a matter of pure style, here, but rather of clarity (e.g. lines 186-188, 202-205, 291-301, and so forth)	Thank you for the specific comments on English Editing. The authors assure that the manuscript is thoroughly checked for the scientific words. The lines mentioned in the comments as well as others are clarified throughout the manuscript. The authors also express the willingness to the journal to carry out English editing if the reviewers are not satisfied with the draft.
2	The second point is about editing, which is rather poor, at times. Typos (e.g. lines 55, 99-100, 137, 262, 389, and so forth) truncated or incomplete sentences (e.g. lines 132, 172-173, 248-249, 283, and so forth) are rather frequent in the present manuscript	All the corrections were carried out in the revised manuscript.
3	I cannot agree with the concept expressed at lines 52-53, because plants diseases are of course just one of the innumerable fields in which metabolomics can assist plant physiologists	The lines 52 – 53 are revised accordingly.
4	I have a curiosity about the paragraph dealing with metabolomics and drug investigation (lines 212-235) …Which is the link among drugs and plants, in the present context? Would the Authors clarify/explain/demonstrate?	Drug investigation part has been deleted
5	I was unable to understand the concept appearing at lines 361-362…In which sense the metabolome is “smaller” than proteome and genome?....Indeed, the logic, as well as the actual biology, could suggest that exactly the contrary is true…Do the 25,000-40,000 variants of a single class of plant “secondary” metabolites, such as terpenoids, thought to be present across the plant kingdom, are to be regarded as a small number?	Number of metabolites compounds is approximately 3000 which is smaller compared to other omics.
6	I would like the Authors to clarify about the differences among the “targeted/untargeted” approaches (e.g. line 75), just to the benefit of the many readers who might be not familiar with those terms/concepts.	Thank you for the comments. As per the reviewers comments we have revised incorporated the difference among the “targeted/untargeted” approaches.
7	About the use of uncommon acronyms, e.g. CE (line75), PGPB (line 340), and so forth, which should be defined in full, upon their first mention in the text	We have checked the manuscript thoroughly and revised.
8	About the compulsive use of the generic terms “etc” (e.g lines 45, 86, and so forth) which should be always avoided, in any scientific manuscript, because it inspires inaccuracy, incompleteness  and hastiness	We have corrected the manuscript as per reviewer suggestions.
9	About the compulsive use of capital letters as the first letters, even in words which do not require them (e.g. the names of metabolites, lines 167, 180, and so forth)	Thank you for the comments. As per the reviewers comments we have revised the manuscript thoroughly.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript has shown significant improvement and can be accepted in its current form.

Comments on the Quality of English Language

The English is fine.

Reviewer 3 Report

Comments and Suggestions for Authors

Reviewer's recommendations concerning the original manuscript have been followed in a satisfactory manner