Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format

Yan Chen; Jennifer W. Gin; Ying Wang; Markus de Raad; Stephen Tan; Nathan J. Hillson; Trent R. Northen; Paul D. Adams; Christopher J. Petzold

doi:10.1371/journal.pone.0288102

Peer Review History

Original SubmissionFebruary 3, 2023
2 May 2023 Decision Letter - Faiz ul-Hassan Nasim, Editor PONE-D-23-03070 Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format PLOS ONE Dear Dr. Petzold, 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 Jun 12 2023 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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(Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: Comments: Abstract: Authors should be refurnished abstract. 1.Authors should be checked grammar “in alkaline chemical buffer” or “in an alkaline chemical buffer”? Introduction: Authors should be rechecked Result sections: 1.You have extracted protein from Gram-positive bacteria species, Gram-negative bacteria species, and non-filamentous fungi species with ̴2x109 cells of biomass from each species but why did Gram-positive bacteria species total protein obtained very less than Gram-negative species and non-filamentous?. Does protein extraction concentration depend on species? Any specification on the extraction? 2.Haven’t tested any animal cell line/tissues. You should test on primary cells or cell lines because that is good for justification for microbial protocol. The author should at least do the test on either animal tissues/primary cells/cell lines. It may be not applicable to animal cells. Figure Captions: 1.Fig.1: Error bars should be represented by a minimum of three replicates performed on a separate day. Any justification for why the authors' error bars represented two replicates performed/experiments? Reviewer #2: Although the authors have given the reference of the protocol in materials and method section, It will be better to describe the protocol here as well. So that It will make the draft convenient for the readers to assess the total information at one place. The results mentioned were actual results so heading must be changed from expected to more suitable word, or Just 'Results'. Please elaborate the statement ' With two ODmL (~2 ×109 cells) of biomass,' in the expected results section, as it is not clear. ******* 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 #1: Yes: Dr. Aabid Hussain Reviewer #2: Yes: Dr. Adnan Akhter ******** [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. Attachments Attachment Submitted filename: PONE-D-23-03070_reviewer comments.pdf Attachment Submitted filename: PONE-D-23-03070_reviewed.pdf https://doi.org/10.1371/journal.pone.0288102.r001
Revision 1
8 Jun 2023 Author Response Response to Reviewers: Manuscript Number PONE-D-23-03070 Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format Recommendation: Publish after resubmission. Comments: Abstract: Authors should be refurnished abstract. 1. Authors should be checked grammar “in alkaline chemical buffer” or “in an alkaline chemical buffer”? --We corrected the grammar as the reviewer suggested. Introduction: Authors should be rechecked Result sections: 1. You have extracted protein from Gram-positive bacteria species, Gram-negative bacteria species, and non-filamentous fungi species with ̴2x109 cells of biomass from each species but why did Gram-positive bacteria species total protein obtained very less than Gram-negative species and non-filamentous?. Does protein extraction concentration depend on species? Any specification on the extraction? --We thank the reviewer for the question. Yes, the total protein obtained varies depending on the species. Gram-positive bacteria have a thicker cell wall than Gram-negative bacteria, consequently, the percentage of protein is lower for the Gram-positive bacteria on a per cell basis and, correspondingly, for the OD measurements. We clarified this point in the text by adding this statement: “The amount of protein extracted from the microbes will depend on the species of interest, consequently the starting amount of biomass may need to be adjusted for a given application.” 2. Haven’t tested any animal cell line/tissues. You should test on primary cells or cell lines because that is good for justification for microbial protocol. The author should at least do the test on either animal tissues/primary cells/cell lines. It may be not applicable to animal cells. --We thank the reviewer for the suggestion, however, testing on animal cells is beyond the scope of our research and our available resources. This protocol has been tested and applied for microbe analysis because that is the focus of our research, but the reviewer is correct that it may not be applicable to animal cells. Figure Captions: 1. Fig.1: Error bars should be represented by a minimum of three replicates performed on a separate day. Any justification for why the authors' error bars represented two replicates performed/experiments? --For the protein quantification measurements, we decided to examine a larger number of conditions at the expense of the number of replicates. We recollected the data with three replicates to alleviate this concern. Figure 1 is updated with the triplicate measurements and the values have been updated in the text. https://doi.org/10.1371/journal.pone.0288102.r002
20 Jun 2023 Decision Letter - Faiz ul-Hassan Nasim, Editor Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format PONE-D-23-03070R1 Dear Dr. Petzold, 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, Faiz ul-Hassan Nasim, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0288102.r003
Formally Accepted
28 Jun 2023 Acceptance Letter - Faiz ul-Hassan Nasim, Editor PONE-D-23-03070R1 Alkaline-SDS cell lysis of microbes with acetone protein precipitation for proteomic sample preparation in 96-well plate format Dear Dr. Petzold: 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. Faiz ul-Hassan Nasim Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0288102.r004

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