PONE-D-23-21176Human and animal skin identified by palaeoproteomics in Scythian leather objects from UkrainePLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. 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 #1: Partly

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

Reviewer #2: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available?

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Reviewer #1: Yes

Reviewer #2: Yes

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4. Is the manuscript presented in an intelligible fashion and written in standard English?

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Reviewer #1: Yes

Reviewer #2: Yes

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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 manuscript “Human and animal skin identified by palaeoproteomics in Scythian leather objects from Ukraine” is an interesting application of ZooMS and LC-MS/MS for leather identification. The archaeological context, objects and interpretation of the data are well described. The results are however rushed and the paper would benefit from further details. More specifically:

There is a microscopy paragraph in Methods. The paragraph describes results rather than the method employed. Either this paragraph should be moved to results and detailed or removed entirely.

In LC-MS/MS methods, you mention searching the samples against a Swissprot database, and later that “iterative searches were made to narrow down the database to the relevant proteins from the relevant species.” This was repeated in Supplementary but no further detail is provided. The accession numbers in Supplementary for samples 48 and 49 appeared to be from NCBI. Please provide more precision on which databases were searched.

I could not find Figures S2… I only have access to S1.pdf and S1.dataset

The results paragraph is very short and some information provided in Supplementary could be moved there to offer more insights into the results.

In the species identification paragraph, it would be helpful if you could indicate the sample number when you describe specific samples, especially for the wild carnivores. I would also indicate somewhere the common name of species alongside the Latin names (in Supplementary tables as well).

It is unfortunate that only one human sample was analyzed by LC-MS/MS. The sample was chosen due to low resolution by ZooMS. It would have been interesting to compare the results on both samples by LC-MS/MS to understand why one was of lower quality. Furthermore, you have 26% of unidentified samples, which is quite high. Do you have any clues to explain the unidentified samples? Is this a problem with the method, the context in which objects were found, treatment of the leather or preservation issues?

Tables S7 and S8 have the wrong descriptions and one is missing sample name.

Table 3: “Number of proteins and corresponding proteins”. I suppose you mean corresponding peptides.

In discussion, since you mostly talk about quivers, it would be useful to have a drawing showing the different parts of the quiver. While you might not know which part of the object each sample corresponds to, as much as possible, some discussion between the species identified and corresponding part of the object would help to put the results into light. Perhaps as highlighted in a drawing/figure.

Reviewer #2: This is a very interesting study on identifying the species of origin for Scythian leather artefacts using both PMF and LC-MS-based approaches. The study is methodologically sound and the manuscript is very well written with a clear, logical flow. However, there are some minor comments that I believe the authors should consider.

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Figure 2:

Do the scale bars depict cm units? Maybe add a brief sentence to the figure caption for clarification.

Results:

Inconsistency – Table 2 reads “Kurgan 4, burial 2” for sample 7 from Ilyinka which was identified as human, however the main text referring to this sample reads “kurgan 2, burial 4”. This is seen again in Figure 5 caption which also reads "kurgan 2, burial 4". Based on what the authors have presented in Table 1, should the site read "kurgan 4, burial 2" in all instances?

Supplementary Information:

Reference is made in the Methods (section Liquid chromatography-tandem mass spectrometry) and Supplementary Information S1 to Supplementary Information S2 representing spectral annotations, however S2 doesn't seem to be attached to the current manuscript submission.

Minor typographical corrections:

Orphaned round bracket “)” and extra square bracket “]” in the following Introduction sentence:

“For the purpose of the present study, Scythians are understood to be the nomads that occupied the steppes north of the Black Sea, and between the Danube and the Don Rivers, as defined by the ancient Greek ‘father of history’ Herodotus [17–19]])”

Figure 3 caption: Random comma and space after image credit.

Table 2 caption: Mustela should be italicised and capitalised as it is a genus name.

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Reviewer #1: No

Reviewer #2: No

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Human and animal skin identified by palaeoproteomics in Scythian leather objects from Ukraine

PONE-D-23-21176R1

Dear Dr. Gleba,

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.

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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 #1: All comments have been addressed

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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 #1: Yes

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3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: N/A

**********

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 #1: Yes

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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 #1: Yes

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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 #1: (No Response)

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Reviewer #1: No

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