Journal of Proteome Data and Methods

AIMS & SCOPE

The Journal of Proteome Data and Methods is dedicated to publishing standardized accounts of original proteomics data and datasets, as well as the protocols used to derive and utilize them. It is international, Open Access, and fully peer-reviewed. Launched by the Japanese Proteomics Society, the journal aims to improve the documentation, management and re-use of proteome data. The journal also enables authors to receive credit for their data-based work, while also helping develop the proteomics research infrastructure.

The Journal of Proteome Data and Methods covers the broad range of research disciplines in proteomics: e.g. top-down, middle-down or bottom-up proteomics with data-dependent acquisition, selected reaction monitoring, parallel reaction monitoring and data-independent acquisition. The journal publishes Data Descriptor, which provide detailed descriptions of research data or datasets; Protocol, which describe the experimental procedures used to generate proteome data; Data Processing Note, which describe the algorithms and software used in proteome data analysis; and Review, which present novel or unique overviews of recent or important developments in proteomics.

Submissions must be scientifically important and original, but any technically proficient article that contributes to proteome science is welcomed. The journal also considers submissions that describe historically valuable data or datasets, or experimental protocols and computational methods that have not previously been formally described. To ensure rapid publication, articles are published online as soon as they become available.

MANUSCRIPT TYPES

The journal publishes four article types: Data Descriptor, Protocol, Data Processing Note, and Review.

Data Descriptor is detailed descriptions of a dataset’s metadata, as posted in jPOST or another recognized repository. The descriptions include the culture conditions, the procedures for the preparation of samples and their modification, the settings of each experiment device, and the relationships between experiments and data files. This information is in addition to details of biological samples and liquid chromatograph - mass spectrometer information, which must already be in the metadata for the original submission to the repository.

Protocol is detailed, step-by-step descriptions of the experimental procedures used to generate proteome data, which the authors have tested and standardized. Proteome experiments use a broad range of methods and devices for sample preparation, data collection and data analysis, and the journal is keen to facilitate the wide sharing of these techniques and tips.

Data Processing Note is detailed descriptions of the computational procedures used to analyze proteome data, including software and web tools. Once proteome data have been produced, various procedures – such as quality checks, peak pickings, peptide/protein identification and quantification, and detection of modifications – are used to derive scientific knowledge. By describing the algorithms and procedures used to analyze proteome data, the journal aims to improve the re-use of these data.

Review is an article presenting novel or unique overviews of recent and important developments in proteomics. Review must present clear and original insights into the questions of interest, using appropriate and fully presented evidence; long, general summaries are not published. Review is approximately 5000 words and can investigate several aspects of importance in a subject area. Review is by invitation only, but the journal welcomes proposals from authors. If the proposal meets the criteria of the Journal of Proteome Data and Methods, the Editor-in-Chief will invite the proponent to be the author of the Review.

MANUSCRIPT SUBMISSION

All manuscripts must be submitted via the journal’s online submission system, ScholarOne Manuscripts: https://mc.manuscriptcentral.com/jpdm. The original or revised manuscript text may be uploaded as a PDF or Microsoft Word file, but a Word file is required for the final manuscript text. Figures may be submitted separately in several other formats.

If you encounter any problems with online submission, please contact the Editorial Office: jpdm-office@jhupo.org.

MANUSCRIPT PREPARATION

English standards

Manuscripts should be written in clear, grammatically correct English. Authors whose native language is not English are strongly encouraged to have their manuscript checked by a native English speaker or by an editing service prior to submission. If a manuscript is not clear due to poor English, it may be returned to the authors without undergoing peer review.

Format

The format of each article type is outlined below. Further specifications about each type’s particular sections are then detailed in the following pages.

Title

The title should describe the content of the article briefly but clearly, which is important for searching by third-party services. Do not use the same main title with numbered minor titles, even for a series of papers by the same authors. Do not use abbreviations in the title, except those used generally in related fields.

Authors

Provide the full names, with initials, of the author(s). The journal encourages the use of ORCID iDs, and the identifier of each author should be provided during the submission process, where possible.

Affiliations

Provide full names and addresses of institutions (including laboratory, department, institute and/or university, city, state and country). Affiliation(s) with different institutions should be indicated by superscript numbers. When authors have new affiliations, they should be given in a footnote and should be indicated by superscript symbols (such as * and **).

Key words

A maximum of five key words should be provided.

Repository and Identifier(s) of dataset

The repository name (e.g. jPOST, PRIDE, etc.) and identifier(s) (such as PXDxxxxxx) of the dataset described in the manuscript must be provided for Data Descriptor. For other article types, if any data or dataset(s) were used in the article, please provide the repository and identifier(s).

Abstract

The Abstract should clearly express the basic content of the paper in a single paragraph. Abstracts must not exceed 250 words for all article types. Avoid using specific abbreviations. If it is vital to reference a previous publication, do not include the article title (e.g. Ogata K., Krokhin O. V., and Ishihama Y. (2018). Anal. Sci., 34: 1037-1041).

For Data Descriptor, the Abstract should include the purpose of acquisition of data and a brief description of the experimental approach.

For Protocol and Data Processing Note, the Abstract should include descriptions of the novelty of the methods or experimental/computational approach, main results and conclusions.

Introduction

For all article types, the Introduction should provide sufficient background information to allow the reader to understand the purpose of the investigation, although it should not include an extensive review of the literature.

The above sections are common to all article types. The following sections outline the differences between article types.

Data Descriptor

Data Descriptions

The main Data Description section must describe the content that has been deposited and registered in the repository. In addition, authors must provide details about the data being described, as per the sub-sections below. In order to satisfy the journal’s metadata criteria, the authors must comply with the metadata checklist. View the template and sample files for metadata checklist.

Samples

The source of origin of the samples and their culture conditions should be described. The authors should provide not only species but also appropriate details on tissues, cell types and disease conditions.

Sample pretreatment for MS analysis

The sample processing methods and conditions should be described. For example, the extraction of sub-organelles, enrichment processes, separation of proteins or peptides, and fractionation of the samples.

MS analysis

The following must be provided: mass spectrometer model name, manufacturer, instrument mode (e.g. DDA-high resolution), purpose of measurements (e.g. relative quantification), quantitation method (e.g. spectral counting, SILAC and TMT) and the detailed parameters of the operations.

Data analysis

The relationships between samples and data files must be described in detail. Authors should take special care to accurately describe the correspondence between samples and labels such as SILAC and TMT. In addition, the enzyme (e.g. trypsin) and both fixed and variable modifications used for mass measurement should be described in detail, along with the reaction conditions.

Protocol, Data Processing Note and Review

Materials and Methods

For these article types, the description of the data acquisition or newly proposed methods should be in sufficient detail to allow the experiments to be repeated. In addition, the sources of unusual chemicals, animals, microbial strains or equipment should be described, and the location (city, country) of the supplier should be provided in parentheses. If hazardous materials or dangerous procedures are used in the experiments and the precautions related to their handling are not widely recognized, it is recommended that the authors provide the necessary details. Software developed and presented by the authors in the manuscript must be registered in a public repository such as GitHub and the link provided in the main text.

Results

This section should describe the results of the research. The Results and Discussion sections may be combined if this helps readers to understand and evaluate the study. Tables and figures, including photographs, can be used to present the experimental results (see below). Excessive explanations of the data presented in tables and figures should be avoided.

Discussion

The Discussion should be concise and limited to interpretation of the results. Do not repeat the description of the experimental results in this section.

Conclusion

Authors can include a brief Conclusion that summarizes the overall outcomes of the study.

Tables

Number tables consecutively using Arabic numbers (1, 2, 3, etc.). A title should be given to each table, and it must use capital letters. Explanatory material and footnotes should be typed below the table and should be designated with superscript letters, such as a) or b). Units of measurement should be included with numerical values at the top of columns. Avoid detailed explanations of the experimental conditions used to obtain the data shown in tables; this information should be included in the Materials and Methods section instead.

Figures

Figures include line drawings and photographs. Single-column figures must not exceed 84 mm x 220 mm. Double-column figures must not exceed 173 mm x 220 mm. Magnifications of photographs should be indicated in the legends and/or by scales included in the photographs. Illustrations must be self-explanatory and they should be numbered consecutively with Arabic numerals (i.e. Fig. 1, Fig. 2, etc.). Each figure should have a short title. Figure legends should be typed together in a separate sheet(s). Figure legends should include sufficient experimental details to make the figures intelligible; however, duplicating the descriptions provided in the Materials and Methods should be avoided.

Supplementary Material

Supplementary material adds, but is not essential, to a reader’s understanding of a manuscript. Supplementary material may comprise data, text, audio or video files, and is published online alongside the accepted manuscript.

As supplementary material is peer-reviewed, authors must submit it in its final form as part of their manuscript submission. After a manuscript has been accepted for publication, authors may not make any changes to the supplementary material.

The following sections should be included in all article types.

Acknowledgments

This section should be brief. Authors should list all funding sources for their work in the Acknowledgments section.

References

References should be cited in the text by number, which is in the order of appearance with superscript (e.g. 1). Links to web sites should be cited in the main text but not the References section. All the references must be placed together in a list at the end of the manuscript text. This style is the same as ACS style used in JACS.

Abbreviations

Each abbreviation should be defined in parentheses together with its non-abbreviated term when it first appears in the text (except in the Title and Abstract). Common abbreviations that may be used without any explanation can be found here.

ACCEPTED MANUSCRIPTS

Manuscripts that are accepted for publication are copyedited and typeset by the journal’s production team before publication. All communication regarding accepted manuscripts is with the corresponding author.

Proofs

Page proofs are sent to the corresponding author, who should check and return them within 48 hours. Only essential corrections to typesetting errors or omissions are accepted; excessive changes are not permitted at the proofing stage.

JOURNAL & ETHICS POLICIES

The Journal of Proteome Data and Methods looks to uphold the highest standards in scholarly publishing.

Before submitting a manuscript to the journal, authors must ensure that they have read and complied with the journal’s policies. The journal reserves the right to reject without review any manuscript that the Editor-in-Chief believes may not comply with these policies.

The responsibilities of the journal’s authors, editors, reviewers and publisher regarding research and publication ethics are described in full in the Journal & Ethics Policies.

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

The Journal of Proteome Data and Methods is a data journal and recognizes that clear, standardized and discoverable descriptions of data will speed progress in the field. The journal envisions clear roles for the following elements within proteomics: data repositories, such as jPOST or others within ProteomeXchange, contain the raw and processed data and datasets; the Journal of Proteome Data and Methods contains the metadata and descriptions of raw and processed data, which has been assessed for technical proficiency; and, lastly, more general proteomics or other scholarly journals will contain the wider context, interpretation and discussion of the various raw and processed data.

Therefore, if the description of the data and/or datasets within a submission is original and has not been previously published or otherwise submitted for publication, the journal will consider it for publication (which will generally be as part of the Data Descriptor article type). It is not considered a duplicate submission if the data have been deposited or registered in a repository and/or have been analyzed and interpreted in a separate publication. Authors can obtain clarification by writing to the Editor-in-Chief.

Note that the availability of a manuscript on a publicly accessible preprint server does not constitute prior publication (see ‘Preprints’). Authors must not submit the same, or similar, manuscript elsewhere while the submission is under consideration.

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; be able to 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 Acknowledgments 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 Source Codes

Authors must submit the datasets into any repositories affiliated with the ProteomeXchange Consortium such as jPOST, PRIDE, PeptideAtlas, MassIVE, iProX or Panorama Public and indicate the accession number in the manuscript.

Authors must make their own source code available by linking from their manuscript to relevant community-recognized digital repositories such as GitHub.

All datasets and source codes 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 datasets and source codes 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.

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, 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 Acknowledgments 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.

Self-Archiving (Green Open Access) Policy

Self-archiving, also known as Green Open Access, enables authors to deposit a copy of their manuscript in an online repository. The Journal of Proteome Data and Methods encourages authors of original research manuscripts to upload their article to an institutional or public repository immediately after publication in the journal. For more information about re-use rights, please see the Frequently Asked Questions (FAQs).

PEER REVIEW PROCESS

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. Manuscripts that pass through the initial screening 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, and they are directed to the journal’s Guide to 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 re-submit 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 judgment 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 or declares a relationship to 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.

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.

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

The Japanese Proteomics Society has granted the journal’s Editorial Board complete and sole responsibility for all editorial decisions. The 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.

OPEN ACCESS

The journal has a fully Open Access publication model. For more detailed information on the journal’s Open Access policies, see the Frequently Asked Questions (FAQs).

Article Processing Charge

During the launch phase of the Journal of Proteome Data and Methods, the journal will be supported by society funds and will be free for authors to publish and for readers to access. The journal will instigate an APC at a suitable future time to ensure its ongoing sustainability.

License to Publish

Authors retain copyright in their work but are required to sign a License to Publish to grant the Japanese Proteomics Society various rights, which include publishing the work in the journal under a Creative Commons license.

Creative Commons Licenses

All articles in the journal are Open Access and are published under the terms of the Creative Commons Attribution (CC BY) 4.0 International license. For more information about the license, see the Frequently Asked Questions (FAQs).