Making MALDI-TOF MS for entomological parameters accessible: A practical guide for in-house library creation

Jonathan Karisa; Mercy Tuwei; Kelly Ominde; Brian Bartilol; Zedekiah Ondieki; Haron Musani; Martin Rono; Charles Mbogo; Philip Bejon; Joseph Mwangangi; Caroline Wanjiku; Marta Maia

doi:10.1371/journal.pone.0330605

Peer Review History

Original SubmissionApril 22, 2025
26 May 2025 Decision Letter - Dina Aboelsoued, Editor Dear Dr. Karisa, 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. ============================== The procedures and results reported in this manuscript have largely been been published previously (https://doi.org/10.12688/wellcomeopenres.18982.2) and the added value of this article appears somewhat limited. In the abstract section, the authors wrote "Libraries are built in-house for institutional usage, although a multi-user platform with sharing of spectra and data would be attractive, it is not yet available." This sentence is erroneous and should revised, providing references to published studies that strived to develop a free identification service available online (https://doi.org/10.1371/journal.pone.0305167), a free open-source data analysis pipeline and share mass spectral data (https://doi.org/10.1186/s13071-024-06655-1). I would also strongly recommend to the authors to deposit the mass spectra on a public repository to facilitate the widespread uptake of MALDI-TOF MS for mosquito species identification. ============================== Please submit your revised manuscript by Jul 10 2025 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. A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Dina Aboelsoued, Ph.D. Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note you have not yet provided a protocols.io PDF version of your protocol and/or a protocols.io DOI. 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When submitting your protocol to the protocol entry service please include the customer code PLOS2022 in the Note field and indicate that your protocol is associated with a PLOS ONE Lab Protocol Submission. You should also include the title and manuscript number of your PLOS ONE submission. 3. Thank you for stating the following financial disclosure: “MM - Investment 057212 - Bill and Melinda Gates Foundation - USA MR - FLR_R1_190497 - The Royal Society FLAIR fellowship grant- UK” Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. 4. We noted in your submission details that a portion of your manuscript may have been presented or published elsewhere. “Utility of MALDI-TOF MS for determination of species identity and blood meal sources of primary malaria vectors on the Kenyan coast” in Wellcome Open Research (10.12688/wellcomeopenres.18982.2).“ Please clarify whether this [conference proceeding or publication] was peer-reviewed and formally published. If this work was previously peer-reviewed and published, in the cover letter please provide the reason that this work does not constitute dual publication and should be included in the current manuscript. 5. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. 6. 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. Additional Editor Comments: The procedures and results reported in this manuscript have largely been been published previously (https://doi.org/10.12688/wellcomeopenres.18982.2) and the added value of this article appears somewhat limited. In the abstract section, the authors wrote "Libraries are built in-house for institutional usage, although a multi-user platform with sharing of spectra and data would be attractive, it is not yet available." This sentence is erroneous and should revised, providing references to published studies that strived to develop a free identification service available online (https://doi.org/10.1371/journal.pone.0305167), a free open-source data analysis pipeline and share mass spectral data (https://doi.org/10.1186/s13071-024-06655-1). I would also strongly recommend to the authors to deposit the mass spectra on a public repository to facilitate the widespread uptake of MALDI-TOF MS for mosquito species identification. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author ?> Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the protocol been described in sufficient detail??> To answer this question, please click the link to protocols.io in the Materials and Methods section of the manuscript (if a link has been provided) or consult the step-by-step protocol in the Supporting Information files. Reviewer #1: Yes Reviewer #2: Yes ****** 3. Does the protocol describe a validated method??> Reviewer #1: Yes Reviewer #2: Yes ****** 4. If the manuscript contains new data, have the authors made this data fully available??> The PLOS Data policy Reviewer #1: No Reviewer #2: Yes ****** 5. Is the article presented in an intelligible fashion and written in standard English? Reviewer #1: Yes Reviewer #2: Yes ****** Reviewer #1: In this protocol paper, the authors present a method to develop reference databases for Anopheles species identification with MALDI-TOF MS in-house. The procedures and results reported in this manuscript have largely been been published previously (https://doi.org/10.12688/wellcomeopenres.18982.2) and the added value of this article appears somewhat limited. In the abstract section, the authors wrote "Libraries are built in-house for institutional usage, although a multi-user platform with sharing of spectra and data would be attractive, it is not yet available." This sentence is erroneous and should revised, providing references to published studies that strived to develop a free identification service available online (https://doi.org/10.1371/journal.pone.0305167), a free open-source data analysis pipeline and share mass spectral data (https://doi.org/10.1186/s13071-024-06655-1). I would also strongly recommend to the authors to deposit the mass spectra on a public repository to facilitate the widespread uptake of MALDI-TOF MS for mosquito species identification. Reviewer #2: The Lab Protocol titled " Making MALDI-TOF MS for entomological parameters accessible: A practical guide for in-house library creation was interesting and provided valuable information for readers. It will be publishable ****** 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 https://doi.org/10.1371/journal.pone.0330605.r002
Revision 1
7 Jul 2025 Author Response Comments and response 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The manuscript and associated figures and supplementary documents have been edited and aligned as per the PLOS ONE requirements 2. We note you have not yet provided a protocols.io PDF version of your protocol and/or a protocols.io DOI. When you submit your revision, please provide a PDF version of your protocol as generated by protocols.io (the file will have the protocols.io logo in the upper right corner of the first page) as a Supporting Information file. The filename should be S1_file.pdf, and you should enter “S1 File” into the Description field. Any additional protocols should be numbered S2, S3, and so on. Please also follow the instructions for Supporting Information captions [https://journals.plos.org/plosone/s/supporting-information#loc-captions]. The title in the caption should read: “Step-by-step protocol, also available on protocols.io.” Please assign your protocol a protocols.io DOI, if you have not already done so, and include the following line in the Materials and Methods section of your manuscript: “The protocol described in this peer-reviewed article is published on protocols.io (https://dx.doi.org/10.17504/protocols.io.[...]) and is included for printing purposes as S1 File.” You should also supply the DOI in the Protocols.io DOI field of the submission form when you submit your revision. If you have not yet uploaded your protocol to protocols.io, you are invited to use the platform’s protocol entry service [https://www.protocols.io/we-enter-protocols] for doing so, at no charge. Through this service, the team at protocols.io will enter your protocol for you and format it in a way that takes advantage of the platform’s features. When submitting your protocol to the protocol entry service please include the customer code PLOS2022 in the Note field and indicate that your protocol is associated with a PLOS ONE Lab Protocol Submission. You should also include the title and manuscript number of your PLOS ONE submission. The step-by-step protocol of the process here briefly described, is also available on protocols.io (dx.doi.org/10.17504/protocols.io.n2bvjdy3xvk5/v1) and is included as a supplementary file with this article 3. Thank you for stating the following financial disclosure: “MM - Investment 057212 - Bill and Melinda Gates Foundation – USA. MR - FLR_R1_190497 - The Royal Society FLAIR fellowship grant- UK”Please state what role the funders took in the study. If the funders had no role, please state: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." If this statement is not correct you must amend it as needed. Please include this amended Role of Funder statement in your cover letter; we will change the online submission form on your behalf. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript 4. We noted in your submission details that a portion of your manuscript may have been presented or published elsewhere. “Utility of MALDI-TOF MS for determination of species identity and blood meal sources of primary malaria vectors on the Kenyan coast” in Wellcome Open Research (10.12688/wellcomeopenres.18982.2). “Please clarify whether this [conference proceeding or publication] was peer-reviewed and formally published. If this work was previously peer-reviewed and published, in the cover letter please provide the reason that this work does not constitute dual publication and should be included in the current manuscript. Utility of MALDI-TOF MS for determination of species identity and blood meal sources of primary malaria vectors on the Kenyan coast” in Wellcome Open Research (10.12688/wellcomeopenres.18982.2) is a peer reviewed publication. However, the current submission is a methodology manuscript detailing how to build a MALDI-TOF MS library for entomological samples and explaining the various technical steps analytical steps supported by a protocol. Although we present a case study on mosquitoes, this manuscript is relevant to this working on different insect classes. We detail this approach using data from a previously published article on Afro tropical malaria vectors. The present submission differs in scope and objectives from what has been previously published earlier which demonstrated the method’s ability to identify vectors compared to gold standard. The earlier paper has been referenced. The data from the previous published work is shown in this manuscript only as a case study to elucidate how to build the libraries and employ this technology. 5. When completing the data availability statement of the submission form, you indicated that you will make your data available on acceptance. We strongly recommend all authors decide on a data sharing plan before acceptance, as the process can be lengthy and hold up publication timelines. Please note that, though access restrictions are acceptable now, your entire data will need to be made freely accessible if your manuscript is accepted for publication. This policy applies to all data except where public deposition would breach compliance with the protocol approved by your research ethics board. If you are unable to adhere to our open data policy, please kindly revise your statement to explain your reasoning and we will seek the editor's input on an exemption. Please be assured that, once you have provided your new statement, the assessment of your exemption will not hold up the peer review process. All the data related to this publication has been deposited in the Harvard Dataverse. This includes the dataset, and MALDI-TOF MS Main Spectral Profiles (Libraries) for species identification (https://doi.org/10.7910/DVN/VYQFNO37) 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. All the references are per as the PLOS one guidelines Additional Editor Comments: The procedures and results reported in this manuscript have largely been been published previously (https://doi.org/10.12688/wellcomeopenres.18982.2) and the added value of this article appears somewhat limited. The current submission is a methodology manuscript detailing how to build a MALDI-TOF MS library for entomological samples and explaining the various technical steps analytical steps supported by a protocol. Although we present a case study on mosquitoes, this manuscript is relevant to this working on different insect classes. We detail this approach using data from a previously published article on Afro tropical malaria vectors. The present submission differs in scope and objectives from what has been previously published earlier which demonstrated the method’s ability to identify vectors compared to gold standard. The earlier paper has been referenced. The data from the previous published work is shown in this manuscript only as a case study to elucidate how to build the libraries and employ this technology. In the abstract section, the authors wrote "Libraries are built in-house for institutional usage, although a multi-user platform with sharing of spectra and data would be attractive, it is not yet available." This sentence is erroneous and should revised, providing references to published studies that strived to develop a free identification service available online (https://doi.org/10.1371/journal.pone.0305167), a free open-source data analysis pipeline and share mass spectral data (https://doi.org/10.1186/s13071-024-06655-1). The sentence has been revised to read “Libraries are built in-house for institutional usage, although a multi-user platform with sharing of spectra and data would be attractive. Only a few studies have strived to make their libraries publicly available” Moreover, the MALDI-TOF MS Main Spectral Profiles (Libraries) for species identification related to this publication has been deposited in public repository - Harvard Dataverse (https://doi.org/10.7910/DVN/VYQFNO37) I would also strongly recommend to the authors to deposit the mass spectra on a public repository to facilitate the widespread uptake of MALDI-TOF MS for mosquito species identification. The MALDI-TOF MS Main Spectral Profiles (Libraries) for species identification related to this publication has been deposited in public repository i.e. the Harvard Dataverse (https://doi.org/10.7910/DVN/VYQFNO37) for any one with MALDI-TOF MS equipment to adapt and update for their use Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0330605.r003
17 Jul 2025 Decision Letter - Dina Aboelsoued, Editor Dear Dr. Karisa 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 Aug 31 2025 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. A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'. If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols . Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Dina Aboelsoued, Ph.D. Academic Editor PLOS ONE Journal Requirements: If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. There is no requirement to cite these works unless the editor has indicated otherwise. 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. Additional Editor Comments: The present submission demonstrated the method’s ability to identify vectors compared to gold standard. As the earlier paper has been referenced and used to show how to build the libraries and employ this technology. Authors should shorten the details shown in the current manuscript referring to other published work [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.0330605.r004
Revision 2
20 Jul 2025 Author Response Comments and response 1. If the reviewer comments include a recommendation to cite specific previously published works, please review and evaluate these publications to determine whether they are relevant and should be cited. Response – In the previous review, the reviewers recommended two articles: - (https://doi.org/10.1371/journal.pone.0305167), a free open-source data analysis pipeline and share mass spectral data - (https://doi.org/10.1186/s13071-024-06655-1). Upon reviewing these publications, we noted that the methods used differ from ours. Specifically, both studies employed R and Python scripts for post-acquisition spectral processing. In contrast, our study utilized the MALDI-Biotyper® software for spectral processing and analysis. None of these reference have been included in our manuscript. Regarding the recommendation to deposit mass spectra in a public repository, we confirm that all relevant data associated with this study have been deposited in the Harvard Dataverse. This includes both the raw dataset and the MALDI-TOF MS Main Spectral Profiles (MSPs) used for species identification. The data are accessible via the following DOI: https://doi.org/10.7910/DVN/VYQFNO37 2. 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. Response – Following your suggestion on the references cited in our manuscript, we conducted a thorough review of all the references included in the manuscript. We confirm that none of the cited references appear to have been retracted, and all remain accessible through their respective journals or digital repositories. To the best of our knowledge, all references are from peer-reviewed and meet PLOSOne journal requirements. If the editors or reviewers have any specific concerns regarding individual references, we would be happy to address them promptly. 3. The present submission demonstrated the method’s ability to identify vectors compared to gold standard. As the earlier paper has been referenced and used to show how to build the libraries and employ this technology. Authors should shorten the details shown in the current manuscript referring to other published work Response – The manuscript, especially the methods section, has been revised and the relevant published work and step-by-step protocol deposited in protocol.io has been referenced. Attachments Attachment Submitted filename: Response_to_Reviewers_auresp_2.docx https://doi.org/10.1371/journal.pone.0330605.r005
5 Aug 2025 Decision Letter - Dina Aboelsoued, Editor Making MALDI-TOF MS for entomological parameters accessible: A practical guide for in-house library creation PONE-D-25-21203R2 Dear Mr. Jonathan K Karisa 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support . 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, Dina Aboelsoued, Ph.D. Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0330605.r006
Formally Accepted
Acceptance Letter - Dina Aboelsoued, Editor PONE-D-25-21203R2 PLOS ONE Dear Dr. Karisa, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. If we can help with anything else, please email us at customercare@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. Dina Aboelsoued Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0330605.r007

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