Proteomes — Instructions for Authors
- read the Aims & Scope to gain an overview and assess if your manuscript is suitable for this journal;
- use the Microsoft Word template or LaTeX template to prepare your manuscript;
- make sure that issues about publication ethics, research ethics, copyright, authorship, figure formats, data and references format have been appropriately considered;
- ensure that all authors have approved the content of the submitted manuscript.
Types of Publications
Proteomes has no restrictions on the length of manuscripts, provided that the text is concise and comprehensive. Full experimental details must be provided so that the results can be reproduced. Proteomes requires that authors publish all experimental controls and make full datasets available where possible (see the guidelines on Supplementary Materials and references to unpublished data).
Manuscripts submitted to Proteomes should neither been published before nor be under consideration for publication in another journal. The main article types are as follows:
- Articles: Original research manuscripts. The journal considers all original research manuscripts provided that the work reports scientifically sound experiments and provides a substantial amount of new information. Authors should not unnecessarily divide their work into several related manuscripts, although Short Communications of preliminary, but significant, results will be considered. Quality and impact of the study will be considered during peer review.
- Reviews: These provide concise and precise updates on the latest progress made in a given area of research. Systematic reviews should follow the PRISMA guidelines.
Manuscripts for Proteomes should be submitted online at susy.mdpi.com The submitting author, who is generally the corresponding author, is responsible for the manuscript during the submission and peer-review process. The submitting author must ensure that all eligible co-authors have been included in the author list (read the criteria to qualify for authorship) and that they have all read and approved the submitted version of the manuscript. To submit your manuscript, register and log in to the submission website. Once you have registered, click here to go to the submission form for Proteomes. All co-authors can see the manuscript details in the submission system, if they register and log in using the e-mail address provided during manuscript submission.
Accepted File Formats
Authors must use the Microsoft Word template or LaTeX template to prepare their manuscript. Using the template file will substantially shorten the time to complete copy-editing and publication of accepted manuscripts. The total amount of data for all files must not exceed 120 MB. If this is a problem, please contact the editorial office [email protected] Accepted file formats are:
- Microsoft Word: Manuscripts prepared in Microsoft Word must be converted into a single file before submission. When preparing manuscripts in Microsoft Word, the Proteomes Microsoft Word template file must be used. Please insert your graphics (schemes, figures, etc.) in the main text after the paragraph of its first citation.
- LaTeX: Manuscripts prepared in LaTeX must be collated into one ZIP folder (include all source files and images, so that the Editorial Office can recompile the submitted PDF). When preparing manuscripts in LaTeX, please use the Proteomes LaTeX template files. You can now also use the online application writeLaTeX to submit articles directly to Proteomes. The MDPI LaTeX template file should be selected from the writeLaTeX template gallery.
- Supplementary files: May be any format, but it is recommended that you use common, non-proprietary formats where possible (see below for further details).
A cover letter must be included with each manuscript submission. It should be concise and explain why the content of the paper is significant, placing the findings in the context of existing work and why it fits the scope of the journal. Confirm that neither the manuscript nor any parts of its content are currently under consideration or published in another journal. Any prior submissions of the manuscript to MDPI journals must be acknowledged. The names of proposed and excluded reviewers should be provided in the submission system, not in the cover letter.
Note for Authors Funded by the National Institutes of Health (NIH)
This journal automatically deposits papers to PubMed Central after publication of an issue. Authors do not need to separately submit their papers through the NIH Manuscript Submission System (NIHMS, http://nihms.nih.gov/).
- Research manuscripts should comprise:
- Front matter: Title, Author list, Affiliations, Abstract, Keywords
- Research manuscript sections: Introduction, Materials and Methods, Results, Discussion, Conclusions (optional).
- Back matter: Supplementary Materials, Acknowledgments, Author Contributions, Conflicts of Interest, References.
- Review manuscripts should comprise the front matter, literature review sections and the back matter. The template file can also be used to prepare the front and back matter of your review manuscript. It is not necessary to follow the remaining structure. Structured reviews and meta-analyses should use the same structure as research articles and ensure they conform to the PRISMA guidelines.
- Case reports should include a succinct introduction about the general medical condition or relevant symptoms that will be discussed in the case report; the case presentation including all of the relevant de-identified demographic and descriptive information about the patient(s), and a description of the symptoms, diagnosis, treatment, and outcome; a discussion providing context and any necessary explanation of specific treatment decisions; a conclusion briefly outlining the take-home message and the lessons learned.
- Graphical abstract: Authors are encouraged to provide a graphical abstract as a self-explanatory image to appear alongside with the text abstract in the Table of Contents. Figures should be a high quality image in any common image format. Note that images displayed online will be up to 11 by 9 cm on screen and the figure should be clear at this size.
- Abbreviations should be defined in parentheses the first time they appear in the abstract, main text, and in figure or table captions and used consistently thereafter.
- SI Units (International System of Units) should be used. Imperial, US customary and other units should be converted to SI units whenever possible
- Accession numbers of RNA, DNA and protein sequences used in the manuscript should be provided in the Materials and Methods section. Also see the section on Deposition of Sequences and of Expression Data.
- Equations: If you are using Word, please use either the Microsoft Equation Editor or the MathType add-on. Equations should be editable by the editorial office and not appear in a picture format.
- Research Data and supplementary materials: Note that publication of your manuscript implies that you must make all materials, data, and protocols associated with the publication available to readers. Disclose at the submission stage any restrictions on the availability of materials or information. Read the information about Supplementary Materials and Data Deposit for additional guidelines.
- Preregistration: Where authors have preregistered studies or analysis plans, links to the preregistration must be provided in the manuscript.
- Guidelines and standards: MDPI follows standards and guidelines for certain types of research. See https://www.mdpi.com/editorial_process for further information.
These sections should appear in all manuscript types
- Title: The title of your manuscript should be concise, specific and relevant. It should identify if the study reports (human or animal) trial data, or is a systematic review, meta-analysis or replication study. When gene or protein names are included, the abbreviated name rather than full name should be used.
- Author List and Affiliations: Authors' full first and last names must be provided. The initials of any middle names can be added. The PubMed/MEDLINE standard format is used for affiliations: complete address information including city, zip code, state/province, country, and all email addresses. At least one author should be designated as corresponding author, and his or her email address and other details should be included at the end of the affiliation section. Please read the criteria to qualify for authorship.
- Abstract: The abstract should be a total of about 200 words maximum. The abstract should be a single paragraph and should follow the style of structured abstracts, but without headings: 1) Background: Place the question addressed in a broad context and highlight the purpose of the study; 2) Methods: Describe briefly the main methods or treatments applied. Include any relevant preregistration numbers, and species and strains of any animals used. 3) Results: Summarize the article's main findings; and 4) Conclusion: Indicate the main conclusions or interpretations. The abstract should be an objective representation of the article: it must not contain results which are not presented and substantiated in the main text and should not exaggerate the main conclusions.
- Keywords: Three to ten pertinent keywords need to be added after the abstract. We recommend that the keywords are specific to the article, yet reasonably common within the subject discipline.
- Introduction: The introduction should briefly place the study in a broad context and highlight why it is important. It should define the purpose of the work and its significance, including specific hypotheses being tested. The current state of the research field should be reviewed carefully and key publications cited. Please highlight controversial and diverging hypotheses when necessary. Finally, briefly mention the main aim of the work and highlight the main conclusions. Keep the introduction comprehensible to scientists working outside the topic of the paper.
- Materials and Methods: They should be described with sufficient detail to allow others to replicate and build on published results. New methods and protocols should be described in detail while well-established methods can be briefly described and appropriately cited. Give the name and version of any software used and make clear whether computer code used is available. Include any pre-registration codes.
- Results: Provide a concise and precise description of the experimental results, their interpretation as well as the experimental conclusions that can be drawn.
- Discussion: Authors should discuss the results and how they can be interpreted in perspective of previous studies and of the working hypotheses. The findings and their implications should be discussed in the broadest context possible and limitations of the work highlighted. Future research directions may also be mentioned. This section may be combined with Results.
- Conclusions: This section is not mandatory, but can be added to the manuscript if the discussion is unusually long or complex.
- Patents: This section is not mandatory, but may be added if there are patents resulting from the work reported in this manuscript.
- Supplementary Materials: Describe any supplementary material published online alongside the manuscript (figure, tables, video, spreadsheets, etc.). Please indicate the name and title of each element as follows Figure S1: title, Table S1: title, etc.
- Acknowledgments: All sources of funding of the study should be disclosed. Clearly indicate grants that you have received in support of your research work and if you received funds to cover publication costs. Note that some funders will not refund article processing charges (APC) if the funder and grant number are not clearly and correctly identified in the paper. Funding information can be entered separately into the submission system by the authors during submission of their manuscript. Such funding information, if available, will be deposited to FundRef if the manuscript is finally published.
- Author Contributions: Each author is expected to have made substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data; or the creation of new software used in the work; or have drafted the work or substantively revised it; AND has approved the submitted version (and version substantially edited by journal staff that involves the author’s contribution to the study); AND agrees to be personally accountable for the author’s own contributions and for ensuring that questions related to the accuracy or integrity of any part of the work, even ones in which the author was not personally involved, are appropriately investigated, resolved, and documented in the literature.
For research articles with several authors, a short paragraph specifying their individual contributions must be provided. The following statements should be used "Conceptualization, X.X. and Y.Y.; Methodology, X.X.; Software, X.X.; Validation, X.X., Y.Y. and Z.Z.; Formal Analysis, X.X.; Investigation, X.X.; Resources, X.X.; Data Curation, X.X.; Writing – Original Draft Preparation, X.X.; Writing – Review & Editing, X.X.; Visualization, X.X.; Supervision, X.X.; Project Administration, X.X.; Funding Acquisition, Y.Y.”, please turn to the CRediT taxonomy for the term explanation. For more background on CRediT, see here. "Authorship must include and be limited to those who have contributed substantially to the work. Please read the section concerning the criteria to qualify for authorship carefully".
- Conflicts of Interest: Authors must identify and declare any personal circumstances or interest that may be perceived as inappropriately influencing the representation or interpretation of reported research results. If there is no conflict of interest, please state "The authors declare no conflict of interest." Any role of the funding sponsors in the choice of research project; design of the study; in the collection, analyses or interpretation of data; in the writing of the manuscript; or in the decision to publish the results must be declared in this section. Proteomes does not publish studies funded by the tobacco industry. Any projects funded by pharmaceutical or food industries must pay special attention to the full declaration of funder involvement. If there is no role, please state “The sponsors had no role in the design, execution, interpretation, or writing of the study”.
- References: References must be numbered in order of appearance in the text (including table captions and figure legends) and listed individually at the end of the manuscript. We recommend preparing the references with a bibliography software package, such as EndNote, ReferenceManager or Zotero to avoid typing mistakes and duplicated references. We encourage citations to data, computer code and other citable research material. If available online, you may use reference style 9. below.
- Citations and References in Supplementary files are permitted provided that they also appear in the main text and in the reference list.
In the text, reference numbers should be placed in square brackets [ ], and placed before the punctuation; for example , [1–3] or [1,3]. For embedded citations in the text with pagination, use both parentheses and brackets to indicate the reference number and page numbers; for example  (p. 10). or  (pp. 101–105).
References should be described as follows, depending on the type of work:
1. Author 1, A.B.; Author 2, C.D. Title of the article. Abbreviated Journal Name Year, Volume, page range. Available online: URL (accessed on Day Month Year).
2. Author 1, A.; Author 2, B. Book Title, 3rd ed.; Publisher: Publisher Location, Country, Year; pp. 154–196.
3. Author 1, A.; Author 2, B. Title of the chapter. In Book Title, 2nd ed.; Editor 1, A., Editor 2, B., Eds.; Publisher: Publisher Location, Country, Year; Volume 3, pp. 154–196.
4. Author 1, A.B.; Author 2, C. Title of Unpublished Work. status (unpublished; manuscript in preparation).
5. Author 1, A.B.; Author 2, C. Title of Unpublished Work. Abbreviated Journal Name stage of publication (under review; accepted; in press).
6. Author 1, A.B. (University, City, State, Country); Author 2, C. (Institute, City, State, Country). Personal communication, Year.
7. Author 1, A.B.; Author 2, C.D.; Author 3, E.F. Title of Presentation. In Title of the Collected Work (if available), Proceedings of the Name of the Conference, Location of Conference, Country, Date of Conference; Editor 1, Editor 2, Eds. (if available); Publisher: City, Country, Year (if available); Abstract Number (optional), Pagination (optional).
8. Author 1, A.B. Title of Thesis. Level of Thesis, Degree-Granting University, Location of University, Date of Completion.
9. Title of Site. Available online: URL (accessed on Day Month Year).
Unlike published works, websites may change over time or disappear, so we encourage you create an archive of the cited website using a service such as WebCite. Archived websites should be cited using the link provided as follows:
10. Title of Site. URL (archived on Day Month Year).
See the Reference List and Citations Guide for more detailed information.
- File for Figures and schemes must be provided during submission in a single zip archive and at a sufficiently high resolution (minimum 1000 pixels width/height, or a resolution of 300 dpi or higher). Common formats are accepted, however, TIFF, JPEG, EPS and PDF are preferred.
- Proteomes can publish multimedia files in articles or as supplementary materials. Please contact the editorial office for further information.
- All Figures, Schemes and Tables should be inserted into the main text close to their first citation and must be numbered following their number of appearance (Figure 1, Scheme I, Figure 2, Scheme II, Table 1, etc.).
- All Figures, Schemes and Tables should have a short explanatory title and caption.
- All table columns should have an explanatory heading. To facilitate the copy-editing of larger tables, smaller fonts may be used, but no less than 8 pt. in size. Authors should use the Table option of Microsoft Word to create tables.
- Authors are encouraged to prepare figures and schemes in color (RGB at 8-bit per channel). There is no additional cost for publishing full color graphics.
In order to maintain the integrity, transparency and reproducibility of research records, authors must make their experimental and research data openly available either by depositing into data repositories or by publishing the data and files as supplementary information in this journal.
For work where novel computer code was developed, authors should release the code either by depositing in a recognized, public repository or uploading as supplementary information to the publication. The name and version of all software used should be clearly indicated.
Additional data and files can be uploaded as "Supplementary Files" during the manuscript submission process. The supplementary files will also be available to the referees as part of the peer-review process. Any file format is acceptable, however we recommend that common, non-proprietary formats are used where possible.
Restrictions on data availability should be noted during submission and in the manuscript. "Data not shown" should be avoided: authors are encouraged to publish all observations related to the submitted manuscript as Supplementary Material. "Unpublished data" intended for publication in a manuscript that is either planned, "in preparation" or "submitted" but not yet accepted, should be cited in the text and a reference should be added in the References section. "Personal Communication" should also be cited in the text and reference added in the References section. (see also the MDPI reference list and citations style guide).
Data may be deposited with specialized service providers or institutional/subject repositories, preferably those that use the DataCite mechanism. Large data sets and files greater than 60 MB must be deposited in this way. For a list of other repositories specialized in scientific and experimental data, please consult databib.org or re3data.org. The data repository name, link to the data set (URL) and accession number, doi or handle number of the data set must be provided in the paper. The journal Data also accepts submissions of data set papers.
New sequence information must be deposited to the appropriate database prior to submission of the manuscript. Accession numbers provided by the database should be included in the submitted manuscript. Manuscripts will not be published until the accession number is provided.
- New nucleic acid sequences must be deposited in one of the following databases: GenBank, EMBL, or DDBJ. Sequences should be submitted to only one database.
- New high throughput sequencing (HTS) datasets (RNA-seq, ChIP-Seq, degradome analysis, …) must be deposited either in the GEO database or in the NCBI’s Sequence Read Archive.
- New microarray data must be deposited either in the GEO or the ArrayExpress databases.The "Minimal Information About a Microarray Experiment" (MIAME) guidelines published by the Microarray Gene Expression Data Society must be followed.
- New protein sequences obtained by protein sequencing must be submitted to UniProt (submission tool SPIN).
All sequence names and the accession numbers provided by the databases should be provided in the Materials and Methods section of the article.
Citations and References in Supplementary files are permitted provided that they also appear in the reference list of the main text.
Research Involving Human Subjects
When reporting on research that involves human subjects, human material, human tissues, or human data, authors must declare that the investigations were carried out following the rules of the Declaration of Helsinki of 1975 (https://www.wma.net/what-we-do/medical-ethics/declaration-of-helsinki/), revised in 2013. According to point 23 of this declaration, an approval from an ethics committee should have been obtained before undertaking the research. At a minimum, a statement including the project identification code, date of approval and name of the ethics committee or institutional review board should be cited in the Methods Section of the article. Data relating to individual participants must be described in detail, but private information identifying participants need not be included unless the identifiable materials are of relevance to the research (for example, photographs of participants’ faces that show a particular symptom). Editors reserve the right to reject any submission that does not meet these requirements.
Example of an ethical statement: "All subjects gave their informed consent for inclusion before they participated in the study. The study was conducted in accordance with the Declaration of Helsinki, and the protocol was approved by the Ethics Committee of XXX (Project identification code)."
A written informed consent for publication must be obtained from participating patients who can be identified (including by the patients themselves). Patients’ initials or other personal identifiers must not appear in any images. For manuscripts that include any case details, personal information, and/or images of patients, authors must obtain signed informed consent from patients (or their relatives/guardians) before submitting to an MDPI journal. Patient details must be anonymized as far as possible, e.g., do not mention specific age, ethnicity, or occupation where they are not relevant to the conclusions.
A template permission form is available to download. A blank version of the form used to obtain permission (without the patient names or signature) must be uploaded with your submission.
You may refer to our sample form and provide an appropriate form after consulting with your affiliated institution. Alternatively, you may provide a detailed justification of why informed consent is not necessary. For the purposes of publishing in MDPI journals, a consent, permission, or release form should include unlimited permission for publication in all formats (including print, electronic, and online), in sublicensed and reprinted versions (including translations and derived works), and in other works and products under open access license. To respect patients’ and any other individual’s privacy, please do not send signed forms. The journal reserves the right to ask authors to provide signed forms if necessary.
Ethical Guidelines for the Use of Animals in Research
The editors will require that the benefits potentially derived from any research causing harm to animals are significant in relation to any cost endured by animals, and that procedures followed are unlikely to cause offense to the majority of readers. Authors should particularly ensure that their research complies with the commonly-accepted '3Rs':
- Replacement of animals by alternatives wherever possible,
- Reduction in number of animals used, and
- Refinement of experimental conditions and procedures to minimize the harm to animals.
Any experimental work must also have been conducted in accordance with relevant national legislation on the use of animals for research. For further guidance authors should refer to the Code of Practice for the Housing and Care of Animals Used in Scientific Procedures .
Manuscripts containing original descriptions of research conducted in experimental animals must contain details of approval by a properly constituted research ethics committee. As a minimum, the project identification code, date of approval and name of the ethics committee or institutional review board should be cited in the Methods section.
Proteomes endorses the ARRIVE guidelines (www.nc3rs.org.uk/ARRIVE) for reporting experiments using live animals. Authors and reviewers can use the ARRIVE guidelines as a checklist, which can be found at www.nc3rs.org.uk/ARRIVEchecklist.
1. Home Office. Animals (Scientific Procedures) Act 1986. Code of Practice for the Housing and Care of Animals Used in Scientific Procedures. Available online: http://www.official-documents.gov.uk/document/hc8889/hc01/0107/0107.pdf.
Research Involving Cell Lines
Methods sections for submissions reporting on research with cell lines should state the origin of any cell lines. For established cell lines the provenance should be stated and references must also be given to either a published paper or to a commercial source. If previously unpublished de novo cell lines were used, including those gifted from another laboratory, details of institutional review board or ethics committee approval must be given, and confirmation of written informed consent must be provided if the line is of human origin.
An example of Ethical Statements:
The HCT116 cell line was obtained from XXXX. The MLH1+ cell line was provided by XXXXX, Ltd. The DLD-1 cell line was obtained from Dr. XXXX. The DR-GFP and SA-GFP reporter plasmids were obtained from Dr. XXX and the Rad51K133A expression vector was obtained from Dr. XXXX.
Research Involving Plants
Experimental research on plants (either cultivated or wild) including collection of plant material, must comply with institutional, national, or international guidelines. We recommend that authors comply with the Convention on Biological Diversity and the Convention on the Trade in Endangered Species of Wild Fauna and Flora.
For each submitted manuscript supporting genetic information and origin must be provided. For research manuscripts involving rare and non-model plants (other than, e.g., Arabidopsis thaliana, Nicotiana benthamiana, Oriza sativa, or many other typical model plants), voucher specimens must be deposited in an accessible herbarium or museum. Vouchers may be requested for review by future investigators to verify the identity of the material used in the study (especially if taxonomic rearrangements occur in the future). They should include details of the populations sampled on the site of collection (GPS coordinates), date of collection, and document the part(s) used in the study where appropriate. For rare, threatened or endangered species this can be waived but it is necessary for the author to describe this in the cover letter.
Editors reserve the rights to reject any submission that does not meet these requirements.
An example of Ethical Statements:
Torenia fournieri plants were used in this study. White-flowered Crown White (CrW) and violet-flowered Crown Violet (CrV) cultivars selected from ‘Crown Mix’ (XXX Company, City, Country) were kindly provided by Dr. XXX (XXX Institute, City, Country).
Arabidopis mutant lines (SALKxxxx, SAILxxxx,…) were kindly provided by Dr. XXX , institute, city, country).
The editors of this journal enforce a rigorous peer-review process together with strict ethical policies and standards to ensure to add high quality scientific works to the field of scholarly publication. Unfortunately, cases of plagiarism, data falsification, image manipulation, inappropriate authorship credit, and the like, do arise. The editors of Proteomes take such publishing ethics issues very seriously and are trained to proceed in such cases with a zero tolerance policy.
Authors wishing to publish their papers in Proteomes must abide to the following:
- Any facts that might be perceived as a possible conflict of interest of the author(s) must be disclosed in the paper prior to submission.
- Authors should accurately present their research findings and include an objective discussion of the significance of their findings.
- Data and methods used in the research need to be presented in sufficient detail in the paper, so that other researchers can replicate the work.
- Raw data should preferably be publicly deposited by the authors before submission of their manuscript. Authors need to at least have the raw data readily available for presentation to the referees and the editors of the journal, if requested. Authors need to ensure appropriate measures are taken so that raw data is retained in full for a reasonable time after publication.
- Simultaneous submission of manuscripts to more than one journal is not tolerated.
- Republishing content that is not novel is not tolerated (for example, an English translation of a paper that is already published in another language will not be accepted).
- If errors and inaccuracies are found by the authors after publication of their paper, they need to be promptly communicated to the editors of this journal so that appropriate actions can be taken. Please refer to our policy regarding publication of publishing addenda and corrections.
- Your manuscript should not contain any information that has already been published. If you include already published figures or images, please obtain the necessary permission from the copyright holder to publish under the CC-BY license. For further information, see the Rights and Permissions page.
- Plagiarism, data fabrication and image manipulation are not tolerated.
- Plagiarism is not acceptable in Proteomes submissions.
Plagiarism includes copying text, ideas, images, or data from another source, even from your own publications, without giving any credit to the original source.
Reuse of text that is copied from another source must be between quotes and the original source must be cited. If a study's design or the manuscript's structure or language has been inspired by previous works, these works must be explicitly cited.
If plagiarism is detected during the peer review process, the manuscript may be rejected. If plagiarism is detected after publication, we may publish a correction or retract the paper.
- Image files must not be manipulated or adjusted in any way that could lead to misinterpretation of the information provided by the original image.
Irregular manipulation includes: 1) introduction, enhancement, moving, or removing features from the original image; 2) grouping of images that should obviously be presented separately (e.g., from different parts of the same gel, or from different gels); or 3) modifying the contrast, brightness or color balance to obscure, eliminate or enhance some information.
If irregular image manipulation is identified and confirmed during the peer review process, we may reject the manuscript. If irregular image manipulation is identified and confirmed after publication, we may correct or retract the paper.
Our in-house editors will investigate any allegations of publication misconduct and may contact the authors' institutions or funders if necessary. If evidence of misconduct is found, appropriate action will be taken to correct or retract the publication. Authors are expected to comply with the best ethical publication practices when publishing with MDPI.
During the submission process, please suggest three potential reviewers with the appropriate expertise to review the manuscript. The editors will not necessarily approach these referees. Please provide detailed contact information (address, homepage, phone, e-mail address). The proposed referees should neither be current collaborators of the co-authors nor have published with any of the co-authors of the manuscript within the last five years. Proposed reviewers should be from different institutions to the authors. You may identify appropriate Editorial Board members of the journal as potential reviewers. You may suggest reviewers from among the authors that you frequently cite in your paper.
To facilitate proper peer-reviewing of your manuscript, it is essential that it is submitted in grammatically correct English. Advice on some specific language points can be found here.
If you are not a native English speaker, we recommend that you have your manuscript professionally edited before submission or read by a native English-speaking colleague. This can be carried out by MDPI's English editing service. Professional editing will enable reviewers and future readers to more easily read and assess the content of submitted manuscripts. All accepted manuscripts undergo language editing, however an additional fee will be charged to authors if very extensive English corrections must be made by the Editorial Office: pricing is according to the service here.
Proteomes accepts articles that have previously been made available as preprints provided that they have not undergone peer review. A preprint is a draft version of a paper made available online before submission to a journal.
MDPI operates Preprints, a preprint server to which submitted papers can be uploaded directly after completing journal submission. Note that Preprints operates independently of the journal and posting a preprint does not affect the peer review process. Check the Preprints instructions for authors for further information.
Expanded and high quality conference papers can be considered as articles if they fulfil the following requirements: (1) the paper should be expanded to the size of a research article; (2) the conference paper should be cited and noted on the first page of the paper; (3) if the authors do not hold the copyright of the published conference paper, authors should seek the appropriate permission from the copyright holder; (4) authors are asked to disclose that it is conference paper in their cover letter and include a statement on what has been changed compared to the original conference paper. Proteomes does not publish pilot studies or studies with inadequate statistical power.
Each author is expected to have made substantial contributions to the conception or design of the work; acquisition, analysis, or interpretation of data; the creation of new software used in the work; and/or writing or substantively revising the manuscript. In addition, all authors must have approved the submitted version (and any substantially modified version that involves the author’s contribution to the study); AND agrees to be personally accountable for the author’s own contributions and for ensuring that questions related to the accuracy or integrity of any part of the work, even those in which the author was not personally involved, are appropriately investigated, resolved, and documented in the literature. Note that acquisition of funding, collection of data, or general supervision of the research group do not, by themselves, justify authorship.Those who contributed to the work but do not qualify for authorship should be listed in the acknowledgements.
More detailed guidance on authorship is given by the International Council of Medical Journal Editors (ICMJE). The journal also adheres to the standards of the Committee on Publication Ethics (COPE) that "all authors should agree to be listed and should approve the submitted and accepted versions of the publication. Any change to the author list should be approved by all authors including any who have been removed from the list. The corresponding author should act as a point of contact between the editor and the other authors and should keep co-authors informed and involve them in major decisions about the publication (e.g. answering reviewers’ comments)." . We reserve the right to request confirmation that all authors meet the authorship conditions.
- Wager, E.; Kleinert, S. Responsible research publication: international standards for authors. A position statement developed at the 2nd World Conference on Research Integrity, Singapore, July 22-24, 2010. In Promoting Research Integrity in a Global Environment; Mayer, T., Steneck, N., eds.; Imperial College Press / World Scientific Publishing: Singapore; Chapter 50, pp. 309-16.
All submitted manuscripts received by the Editorial Office will be checked by a professional in-house Managing Editor to determine whether they are properly prepared and whether they follow the ethical policies of the journal, including those for human and animal experimentation. Manuscripts that do not fit the journal's ethics policy or do not meet the standards of the journal will be rejected before peer-review. Manuscripts that are not properly prepared will be returned to the authors for revision and resubmission. After these checks, the Managing Editor will consult the journals’ Editor-in-Chief or Associate Editors to determine whether the manuscript fits the scope of the journal and whether it is scientifically sound. No judgment on the potential impact of the work will be made at this stage. Reject decisions at this stage will be verified by the Editor-in-Chief.
Once a manuscript passes the initial checks, it will be assigned to at least two independent experts for peer-review. A single-blind review is applied, where authors' identities are known to reviewers. Peer review comments are confidential and will only be disclosed with the express agreement of the reviewer.
In the case of regular submissions, in-house assistant editors will invite experts, including recommendations by an academic editor. These experts may also include Editorial Board members and Guest Editors of the journal. Potential reviewers suggested by the authors may also be considered. Reviewers should not have published with any of the co-authors during the past five years and should not currently work or collaborate with any of the institutions of the co-authors of the submitted manuscript.
The journal operates optional open peer-review: Authors are given the option for all review reports and editorial decisions to be published alongside their manuscript. In addition, reviewers can sign their review, i.e., identify themselves in the published review reports. Authors can alter their choice for open review at any time before publication, however once the paper has been published changes will only be made at the discretion of the Publisher and Editor-in-Chief. We encourage authors to take advantage of this opportunity as proof of the rigorous process employed in publishing their research. To guarantee an impartial refereeing the names of referees will be revealed only if the referees agree to do so, and after a paper has been accepted for publication.
All the articles, reviews and communications published in MDPI journals go through the peer-review process and receive at least two reviews. The in-house editor will communicate the decision of the academic editor, which will be one of the following:
- Accept after Minor Revisions:
The paper is in principle accepted after revision based on the reviewer’s comments. Authors are given five days for minor revisions.
- Reconsider after Major Revisions:
The acceptance of the manuscript would depend on the revisions. The author needs to provide a point by point response or provide a rebuttal if some of the reviewer’s comments cannot be revised. Usually, only one round of major revisions is allowed. Authors will be asked to resubmit the revised paper within a suitable time frame, and the revised version will be returned to the reviewer for further comments.
- Reject and Encourage Resubmission:
If additional experiments are needed to support the conclusions, the manuscript will be rejected and the authors will be encouraged to re-submit the paper once further experiments have been conducted.
The article has serious flaws, and/or makes no original significant contribution. No offer of resubmission to the journal is provided.
All reviewer comments should be responded to in a point-by-point fashion. Where the authors disagree with a reviewer, they must provide a clear response.
Authors may appeal a rejection by sending an e-mail to the Editorial Office of the journal. The appeal must provide a detailed justification, including point-by-point responses to the reviewers' and/or Editor's comments. The Managing Editor of the journal will forward the manuscript and related information (including the identities of the referees) to the Editor-in-Chief, Associate Editor, or Editorial Board member. The academic Editor being consulted will be asked to give an advisory recommendation on the manuscript and may recommend acceptance, further peer-review, or uphold the original rejection decision. A reject decision at this stage is final and cannot be reversed.
In the case of a special issue, the Managing Editor of the journal will forward the manuscript and related information (including the identities of the referees) to the Editor-in-Chief who will be asked to give an advisory recommendation on the manuscript and may recommend acceptance, further peer-review, or uphold the original rejection decision. A reject decision at this stage will be final and cannot be reversed.
Once accepted, the manuscript will undergo professional copy-editing, English editing, proofreading by the authors, final corrections, pagination, and, publication on the www.mdpi.com website.
Authors are strongly encouraged to pre-register clinical trials with an international clinical trials register or and to cite a reference to the registration in the Methods section. Suitable databases include clinicaltrials.gov, the EU Clinical Trials Register and those listed by the World Health Organisation International Clinical Trials Registry Platform.
Proteomes requires a completed CONSORT 2010 checklist and flow diagram as a condition of submission when reporting the results of a randomized trial. Templates for these can be found here or on the CONSORT website (http://www.consort-statement.org) which also describes several CONSORT checklist extensions for different designs and types of data beyond two group parallel trials. At minimum, your article should report the content addressed by each item of the checklist. Meeting these basic reporting requirements will greatly improve the value of your trial report and may enhance its chances for eventual publication.