Peptide barcodes in dogs affected by mitral valve disease with and without pulmonary hypertension using MALDI-TOF MS and LC-MS/MS

Nattapon Riengvirodkij; Sittiruk Roytrakul; Janthima Jaresitthikunchai; Narumon Phaonakrop; Sawanya Charoenlappanich; Walasinee Sakcamduang

doi:10.1371/journal.pone.0255611

Peer Review History

Original SubmissionApril 3, 2021
24 May 2021 Decision Letter - Joseph Banoub, Editor PONE-D-21-09311 Peptide barcodes in dogs affected by mitral valve disease with and without pulmonary hypertension using MALDI - TOF MS and LC - MS / MS PLOS ONE Dear Dr. Sakcamduang, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process. Please submit your revised manuscript by Jul 05 2021 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. 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Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: I Don't Know Reviewer #2: Yes ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ****** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The authors in this manuscript used mass spectrometry-based proteomics to differentiate between the different stages of mitral valve disease (MVD) found in dogs. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to compare the serum proteomes from healthy dogs, dogs with MVD stage B (MVD B, asymptomatic stage), MVD stage C (MVD C, symptomatic stage), MVD stage B with PH (MVD B PH) and MVD stage C with PH (MVD C PH). This resulted in the identification of the differences in the serum peptide barcodes of dogs in the MVD B, MVD C, MVD B PH, MVD C PH, and normal control groups. Six discriminatory peptides at m/z 1,225.60, 1,363.85, 1,688.71, 1789.52, 2020.21, and 2156.42 were altered in their abundance, representing changes in the protein levels of peptide barcode components among the groups. These results are helpful in the diagnosis of different stages of MVD with PH or without PH (pulmonary hypertension). Overall, I recommend the publication of this work as it demonstrates the application of mass spectrometry-based proteomics in diagnosis. Reviewer #2: The manuscript by Riengvirodkij et al., titled “Peptide barcodes in dogs affected by mitral valve disease with and without pulmonary hypertension using MALDI-TOF MS and LC-MS/MS”, uses mass spectrometry to examine peptides specific to mitral valve disease, without or with pulmonary hypertension. It is an interesting approach, and it appears to be quite accurate in distinguishing MVD without or with hypertension. Specific comments are as follows: 1. Of concern is the choice of the ‘normal’ group, having a median age of about half that of the other groups. Is it possible that some of the barcodes identified could become non-specific to one or more groups if the ‘normal’ group had an increased age? A discussion point on the choice of the ‘normal’ group and limitations of this group with age is needed. 2. A practical limitation would include the access to MALDI and LC equipment to a veterinary clinic. It is very unlikely a clinic would purchase such equipment, thus in several instances the analyses of samples would have to be outsourced. Consider a discussion point about this limitation. 3. Was pro B-type-natriuretic peptide data available for the animals examined? If so, was it also examined via mass spectrometry, and how did the differing methods compare? 4. Minor: though well written, some correction to punctuation is needed through the manuscript. ****** 6. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #1: No Reviewer #2: No [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0255611.r001
Revision 1
2 Jul 2021 Author Response Journal Requirement: Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. We have checked our references and found none of them have been retracted. We deleted reference 11 as it duplicated reference 6 in the previous manuscript (line 519-520 of the track-change file). The revision manuscript then has 58 references relevant the PLOS ONE’s requirements. Reviewer 1: There is no specific concern from reviewer 1. Thank you very much for your consideration recommending the publication of our study. Reviewer 2: 1. Of concern is the choice of the ‘normal’ group, having a median age of about half that of the other groups. Is it possible that some of the barcodes identified could become non-specific to one or more groups if the ‘normal’ group had an increased age? A discussion point on the choice of the ‘normal’ group and limitations of this group with age is needed. Because mitral valve disease and pulmonary hypertension, the conditions we have focused on in this study, are commonly found in older dogs, usually more than 5 years old. Accordingly, we designed to recruit dogs at least 5 years old to match the age between normal and the disease groups. However, despite this attempt, the median age of the normal group was still a half younger than the other groups. The reason for this situation was the lack of aging dogs without any concurrent systemic diseases. Therefore, most of the enrolled dogs in the normal group were much younger than dogs in the group with mitral valve disease and pulmonary hypertension. For this concern, it is still possible that some peptide barcodes of the normal group may become non-specific to the disease group if the normal group has an increased age. This limitation has been additionally discussed as the study’s limitations in the discussion part (line 407-420 of the track-change file, and line 406-420 of the non-track-change file). 2. A practical limitation would include the access to MALDI and LC equipment to a veterinary clinic. It is very unlikely a clinic would purchase such equipment, thus in several instances the analyses of samples would have to be outsourced. Consider a discussion point about this limitation. Presently, MALDI-TOF MS is being used in human medicine as a common diagnostic test for early diagnosis and monitoring, particularly in the field of neoplastic illnesses. It has been used to detect cancer in its early stages in a variety of cancers. Conversely, in veterinary medicine, there is a limitation in reaching MALDI-TOF and LC mass spectrometry in routine practice due to the high cost of the equipment. However, this study could add a point of view in the proteomic field of veterinary cardiology. Although the use of MALDI-TOF as a diagnostic method in dogs with heart diseases is still currently limited in the present day. In the future, the findings of this study may assist in the development of a novel diagnostic method for dogs with heart diseases. We have already added the discussion of this point as a study limitation (line 420-429 of the track-change file, 420-428 of the non-track-change file). 3. Was pro B-type-natriuretic peptide data available for the animals examined? If so, was it also examined via mass spectrometry, and how did the differing methods compare? We have no data available of N-terminal B-type-natriuretic peptides for the enrolled animals in this study. To our knowledge, no study reported on comparing the measurement of N-terminal B-type-natriuretic peptide levels and mass spectrometry as diagnostic methods in dogs with mitral valve disease and pulmonary hypertension. This is an interesting topic that recommends further investigation. 4. Minor: though well written, some correction to punctuation is needed through the manuscript. We thoroughly revised the language usage and punctuation in our manuscript. Attachments Attachment Submitted filename: Response to Reviewers_Final 20210627.pdf https://doi.org/10.1371/journal.pone.0255611.r002
21 Jul 2021 Decision Letter - Joseph Banoub, Editor Peptide barcodes in dogs affected by mitral valve disease with and without pulmonary hypertension using MALDI-TOF MS and LC-MS/MS PONE-D-21-09311R1 Dear Dr. Sakcamduang, We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Joseph Banoub, Ph,D., D. Sc. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #2: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #2: Yes ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #2: Yes ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #2: All comments were addressed; apologies to the authors, as this reviewer missed a commented point in the Discussion. ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review?** For information about this choice, including consent withdrawal, please see our Privacy Policy. Reviewer #2: No https://doi.org/10.1371/journal.pone.0255611.r003
Formally Accepted
29 Jul 2021 Acceptance Letter - Joseph Banoub, Editor PONE-D-21-09311R1 Peptide barcodes in dogs affected by mitral valve disease with and without pulmonary hypertension using MALDI-TOF MS and LC-MS/MS Dear Dr. Sakcamduang: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Joseph Banoub Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0255611.r004

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