The Journal of Proteome Data and Methods upholds the highest standards regarding research and publishing practice. This comprehensive suite of policies covers the main responsibilities of the journal’s authors, reviewers, editors and owner.
Author Responsibilities
Submission
The Journal of Proteome Data and Methods welcomes manuscript submissions from authors based anywhere in the world.
Submission to the journal implies that all authors have read and approved the manuscript, have agreed to its submission, and have the right to publish their work.
Submission to the journal also implies that all authors have read and complied with the journal’s policies on publication ethics. Authors of submitted manuscripts acknowledge that the journal’s editors reserve the right to reject or retract any manuscript that they believe may breach any of these policies.
Duplicate submission
Submission to the journal implies that the manuscript has not been previously published (in part or in whole, in any language), is not in press, and is not under consideration for publication elsewhere.
Authors must inform the editors if any related manuscripts are under consideration, in press or published elsewhere. The availability of a manuscript on a publicly accessible preprint server does not constitute prior publication (see ‘Preprints’).
If authors choose to submit their manuscript elsewhere before a final decision has been made on its suitability for publication in the Journal of Proteome Data and Methods, they should first withdraw it from the Journal of Proteome Data and Methods.
Originality
Submission to the journal implies that the manuscript is original work. The journal may use software to screen manuscripts for unoriginal content. By submitting a manuscript to the journal, authors agree to this screening. Any manuscript with an unacceptable level of unoriginal material may be rejected or retracted at the Editor-in-Chief’s discretion.
Preprints
To support the wide dissemination of research, the journal encourages authors to post their research manuscripts on community-recognized preprint servers, either before or alongside submission to the journal. This policy applies only to the original version of a manuscript that describes primary research. Any version of a manuscript that has been revised in response to reviewers’ comments, accepted for publication or published in the journal should not be posted on a preprint server. Instead, forward links to the published manuscript may be posted on the preprint server.
Scooping
When assessing the novelty of a manuscript submitted to the journal, the editors will not be influenced by other manuscripts that are posted on community-recognized preprint servers after the date of submission to the Journal of Proteome Data and Methods (or after the date of posting on a preprint server, if the manuscript is submitted to the Journal of Proteome Data and Methods within four months).
Authorship
Submission to the journal implies that all authors have seen and approved the author list. Changes to the author list after manuscript submission – such as the insertion or removal of author names, or a rearrangement of author order – must be approved by all authors and the Editor-in-Chief.
Authors are encouraged to consider the Council of Science Editors (CSE) principles governing authorship. According to the CSE guidelines, authors must have made substantial contributions to the work; have agreed to be held accountable for their own contributions to the work; can identify which co-authors are responsible for other parts of the work; have confidence in the integrity of the work; and have reviewed and approved the final manuscript. Contributors who do not qualify for authorship may be included in the Acknowledgements section instead.
Image integrity
Authors may digitally manipulate or process images, but images in a manuscript must accurately reflect the original data from which they derive. Any adjustments must be necessary and minimized, be applied to the entire image, meet scholarly standards, and be transparently and fully described within the manuscript. Authors must not alter, remove, add or enhance individual parts of an image. The editors may request original, unprocessed images from the authors and a failure to provide these images may result in a manuscript being rejected or retracted.
Reproducing copyrighted material
If a manuscript includes material that is not under the authors’ own copyright, the authors must obtain permission from the copyright holder(s) to reproduce it.
If a manuscript includes previously published material, the authors must obtain permission from the copyright owners and the publisher of the original work to reproduce it. The authors must cite the original work in their manuscript.
Copies of all reproduction permissions must be included with the manuscript when it is first submitted.
Availability of data and materials
Authors must disclose the source of publicly available data and materials, such as public repositories or commercial manufacturers, by including accession numbers or company details in their manuscript, as appropriate.
Authors may make their own data and materials available in Supplementary Material, or by linking from their manuscript to relevant community-recognized public databases or digital repositories. All data sets must be made available in full to the editors and reviewers during the peer review process, and must be made publicly available by the date of publication. Authors commit to preserving their data sets for at least five years from the date of publication in the journal.
The journal encourages authors to grant reasonable requests from colleagues to share any data, materials and experimental protocols described in their manuscript.
Animal/human experimentation
Authors of manuscripts describing experiments involving humans or materials derived from humans must demonstrate that the research was undertaken in accordance with the principles embodied in the Declaration of Helsinki, its revisions, and any guidelines of the authors’ institutions. When manuscripts do contain experiments per the above, authors must include a statement that describes the procedures for obtaining informed consent from participants regarding participation in the research and publication of the research.
Authors of manuscripts describing experiments involving animals or materials derived from animals must provide evidence that the collection of samples and research obtained approval from, and complied with, the requirements and/or guidelines of the authors’ institution(s).
Specimen collection
Manuscripts describing the collection of wildlife specimens or samples (e.g. metaproteomics) should include detailed information on their provenance and collection methods. Authors must include a statement in their manuscript describing the relevant ethics guidelines, local laws and collection permits under which the research was conducted.
Clinical trial registration
The journal adheres to the International Committee of Medical Journal Editors (ICMJE) policy on Clinical Trials Registration, which recommends that all clinical trials are registered in a public trials registry at or before the time of first patient enrollment as a condition of consideration for publication. Manuscripts describing clinical trials must include the registration number of the trial and the name of the trial registry.
Reporting guidelines
The journal requires authors to follow the EQUATOR Network’s Reporting Guidelines for health research. Study types include, but are not limited to, randomized trials, observational studies, systematic reviews, qualitative research, diagnostic and prognostic studies, animal pre-clinical studies and study protocols. We suggest only including those that are relevant to the 4 types in JPDM.
When the authors submit an article derived from the Human Proteome Project (HPP), the authors must follow the HPP Data Interpretation Guidelines. For Data Descriptor articles, the journal recommends that authors follow the Minimum Information About a Proteomics Experiment (MIAPE) guidelines.
Conflicts of interest
In the interests of transparency, the journal requires all authors to declare any conflicts of interest in relation to their submitted manuscript. A conflict of interest exists when there are actual, perceived or potential circumstances that could influence an author’s ability to conduct or report research impartially. Potential conflicts include (but are not limited to) competing commercial or financial interests, commercial affiliations, consulting roles, or ownership of stock or equity.
Authors should list all funding sources for their work in the Acknowledgements section of their manuscript.
Confidentiality
The journal maintains the confidentiality of all unpublished manuscripts. By submitting their manuscript to the journal, the authors warrant that they will keep all correspondence about their manuscript (from the Editorial Office, editors and reviewers) strictly confidential.
Editor / Publisher Responsibilities
Editorial and peer review process
The journal uses single-blind peer review.
When a manuscript is submitted to the journal, it is assigned to the Editor-in-Chief, who performs initial screening. Manuscripts that do not fit the journal’s scope or are not deemed suitable for publication are rejected without review. The remaining manuscripts are assigned to a handling Editor who assigns two reviewers to assess each manuscript. Reviewers are selected based on their expertise, reputation and previous experience as peer reviewers. The deadline for submission of the reviewers’ reports varies by article type.
Upon receipt of the two reviewers’ reports, the Editor makes the first decision on the manuscript. If the decision is to request revision of the manuscript, authors are requested to resubmit their revised manuscript within one month. Revised manuscripts submitted after this deadline may be treated as new submissions. The Editor may send revised manuscripts to peer reviewers for their feedback or may use his or her own judgement to assess how closely the authors have followed the Editor’s and the reviewers’ comments on the original manuscript.
The Editor then makes a recommendation to the Editor-in-Chief on the manuscript’s suitability for publication. The Editor-in-Chief is responsible for making the final decision on each manuscript.
The members of the Editorial Committee act in advisory roles, providing feedback as reviewers and making suggestions to improve the journal. In cases where the Editor-in-Chief is an author on a manuscript submitted to the journal, a member of the Editorial Committee is responsible for making the final decision on the manuscript’s suitability for publication in the journal.
The Editor-in-Chief acts as an arbitrator when necessary.
Reviewer suggestions
When submitting a manuscript to the journal, authors may suggest reviewers that they would like included in or excluded from the peer review process. The Editor may consider these suggestions but is under no obligation to follow them. The selection, invitation and assignment of peer reviewers is at the Editor’s sole discretion.
Reviewer reports
It is the journal’s policy to transmit reviewers’ comments to the authors in their original form. However, the journal reserves the right to edit reviewers’ comments, without consulting the reviewers, if they contain offensive language, confidential information or recommendations for publication.
Editorial decisions
If a manuscript satisfies the journal’s requirements and represents a significant contribution to the published literature, the Editor may recommend acceptance for publication in the journal.
If a manuscript does not meet the journal’s requirements for acceptance, but it has a high probability of acceptance after minor or major revision, the Editor may ask the authors to revise it accordingly. Revised manuscripts must be submitted within one month, otherwise they will be treated as new submissions.
If a manuscript does not meet the journal’s requirements for acceptance or revision, the Editor may recommend rejection.
Editorial independence
Japanese Proteomics Society has granted the journal’s Editorial Board complete and sole responsibility for all editorial decisions. Japanese Proteomics Society will not become involved in editorial decisions, except in cases of a fundamental breakdown of process.
Editorial decisions are based only on a manuscript’s scientific merit and are kept completely separate from the journal’s other interests. The authors’ ability to pay any publication charges has no bearing on whether a manuscript is accepted for publication in the journal.
Appeals
Authors who believe that an editorial decision has been made in error may lodge an appeal with the Editorial Office. Appeals are only considered if the authors provide detailed evidence of a misunderstanding or mistake by a reviewer or editor. Appeals are considered carefully by the Editor-in-Chief, whose decision is final.
Confidentiality
The journal maintains the confidentiality of all unpublished manuscripts. Editors will not:
- disclose a reviewer’s identity unless the reviewer makes a reasonable request for such disclosure
- discuss the manuscript or its contents with anyone not directly involved with the manuscript or its peer review
- use any data or information from the manuscript in their own work or publications
- use information obtained from the peer review process to provide an advantage to themselves or anyone else, or to disadvantage any individual or organization.
Conflicts of interest
A conflict of interest exists when there are actual, perceived or potential circumstances that could influence an Editor’s ability to act impartially when assessing a manuscript. Such circumstances might include having a personal or professional relationship with an author, working on the same topic or in direct competition with an author, or having a financial stake in the work or its publication.
Members of the journal’s Editorial Board undertake to declare any conflicts of interest when handling manuscripts. An Editor who declares a conflict of interest is unassigned from the manuscript in question and is replaced by a new Editor.
Errata and retractions
The journal recognizes the importance of maintaining the integrity of published literature.
A published article that contains an error may be corrected through the publication of an Erratum. Errata describe errors that significantly affect the scientific integrity of a publication, the reputation of the authors, or the journal itself. Authors who wish to correct a published article should contact the Editor who handled their manuscript or the Editorial Office with full details of the error(s) and their requested changes. In cases where co-authors disagree over a correction, the Editor-in-Chief may consult the Editorial Board or external peer reviewers for advice. If a Correction is published, any dissenting authors will be noted in the text.
A published article that contains invalid or unreliable results or conclusions, has been published elsewhere, or has infringed codes of conduct (covering research or publication ethics) may be retracted. Individuals who believe that a published article should be retracted are encouraged to contact the journal’s Editorial Office with full details of their concerns. The Editor-in-Chief will investigate further and contact the authors of the published article for their response. In cases where co-authors disagree over a retraction, the Editor-in-Chief may consult the Editorial Board or external peer reviewers for advice. If a Retraction is published, any dissenting authors will be noted in the text.
The decision to publish Errata or Retractions is made at the sole discretion of the Editor-in- Chief.
Editors’ own publications in the journal
Any member of the journal’s Editorial Board who is an author on a submitted manuscript is automatically excluded from the peer review process. Within the journal’s online manuscript submission and tracking system, they will be able to see their manuscript as an author but not as an Editor, thereby maintaining the confidentiality of peer review.
A manuscript authored by an Editor of the Journal of Proteome Data and Methods will be subjected to the same high standards of peer review and editorial decision making as any manuscript submitted to the journal.
Responding to potential ethical breaches
The journal will respond to allegations of ethical breaches by following its own policies and, where possible, the guidelines of the Committee on Publication Ethics.
Reviewer Responsibilities
Confidentiality
As part of their responsibilities, reviewers agree to maintain the confidentiality of unpublished manuscripts at all times. By accepting the invitation to review a manuscript, reviewers agree not to:
- disclose their role in reviewing the manuscript
- reveal their identity to any of the authors of the manuscript
- discuss the manuscript or its contents with anyone not directly involved in the review process
- involve anyone else in the review (for example, a post-doc or PhD student) without first requesting permission from the Editor
- use any data or information from the manuscript in their own work or publications
- use information obtained from the peer review process to provide an advantage to themselves or anyone else, or to disadvantage any individual or organization.
Conflicts of interest
A conflict of interest exists when there are actual, perceived or potential circumstances that could influence a reviewer’s ability to assess a manuscript impartially. Such circumstances might include having a personal or professional relationship with an author, working on the same topic or in direct competition with an author, having a financial stake in the work or its publication, or having seen previous versions of the manuscript.
Editors try to avoid conflicts of interest when inviting reviewers, but it is not always possible to identify potential bias. Reviewers are asked to declare any conflicts of interest to the Editor, who will determine the best course of action.