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Author Guidelines

The Journal of Proteolysis accepts submissions via its own electronic submission management system. Articles must be submitted in MS Word (preferable), Open Office, PDF, RTF or LaTeX document file format. Use Journal of Proteolysis LaTeX class to prepare your paper.

Authors should use the Journal of Proteolysis format described in the Formatting Guide.

Authors can verify that the manuscript has been successfully received by selecting ''Articles Status'' in Author Tools. The manuscript's ID tag should appear along the left-hand side. Following its link will show the status of the manuscript.

Cover Letter Requirements

The cover letter should be approximately one page long (optional) and provides following information:  

  • A brief description of significance and novelty of submitting manuscript (one paragraph)
  • How this paper does related to the field of proteolysis and already published works of others?
  • Description of what kind of article authors submitting to the journal (regular research article, short communication or a review)
  • Indicate the status of submitting manuscript (first submission, revision or any of other previous communications with the Journal of Proteolysis editors regarding your manuscript)
  • Provide the short list of potential reviewers for your paper (2-5 persons) and the list of reviewers that authors consider as having conflict of interest (2-5 persons, optional).
The cover letter should be uploaded in Coments to Editor section at the time of manuscript submitting process.

 REGULAR PAPERS Requirements

Manuscript length for regular papers should not exceed 6000 words (including figure legends, tables and references), Abstract - 300 words; the number of figures and/or tables - no more than 8 (total); the number of references - up to 30. Each figure should not contain more than 4 panels. If manuscript contains more than 8 figures and/or tables, it will increase the publication fee of manuscript on $100 (USD) per additional figure/table.

Manuscript should contain sections listed below in the following order:

  • Manuscript Title (up to 20 words)
  • Authors List
  • Authors Affiliations
  • Abstract (up to 300 words)
  • Introduction
  • Materials and Methods
  • Results and Discussion (with tables, figures and figure legends placed in an appropriate part of the text)
  • Acknowledgments
  • Custom services used in the work (if any)
  • References (up to 30 references)

Manuscript Title

Each significant word in the manuscript title should be capitalized. Use 14pt bold Times New Roman font for the title. The distance from the title to the top of the page is 1.5 inches. The title should not exceed 20 words, but has to be informative to the readers. Abbreviations must be excluded from the title, except from widely recognized ones. Special symbols are not allowed in the title. Leave 0.12 inches of extra space after the title.

Authors list and Authors Affiliations

Authors' names should be listed under the Manuscript Title and should contain the following information: first name or initial, middle name as initial and last names. Use 12pt bold Times New Roman font for author name.

For each author his/her affiliation should be specified and listed below authors list including:

  • The name of department, university, company or other affiliated organization
  • Address (city, state and country) of organization
  • One author (or in the case of equal contribution - two authors) has to be chosen as a corresponding author(s) (current e-mail address, telephone and fax numbers for contact have to be provided next to the information about corresponding author affiliation).  Corresponding author is responsible to have an agreement with all other authors about manuscript preparation and publication as well as communication with editors of Journal of Proteolysis.  All authors have to be notified by corresponding author that they have responsibility for the content of submitted manuscript.
  • Use 10pt italic Times New Roman font for institution, address and e-mail.
Abstract

The abstract should summarize the most important context, content and conclusions of the paper in less than 300 words. It should not contain any reference citations, methodological details or displayed equations. Special symbols are not allowed in the abstract. Use 11pt Times New Roman font for abstract text; 12pt bold Times New Roman font for abstract heading. Abstract text is left- and right-justified, 5.5 inches width with the fixed line spacing of 0.17 inches.

Up to five keywords should be provided in the keyword section following the abstract, of which at least two do not appear in the title. Abbreviations have to be listed in abbreviations footnote section following the keywords section.

Introduction

Authors need briefly provide background information about purpose of the study, its significance and importance, and also its relationship to the works of other research groups in the field.

The introduction should not be longer than 600 words. Use 11pt Times New Roman font for Introduction text; 12pt bold Times New Roman font for Introduction heading.

Materials and Methods

The Materials and Methods section should provide the short description of the main materials and methods used in the work by authors. This information has to be sufficiently complete and allow other research groups reproduce and repeat the experiments.  Well established and previously published protocols have to be referenced.

Use 11pt Times New Roman font for Materials and Methods text; 12pt bold Times New Roman font for Materials and Methods heading.

Results and Discussion

This section should present the results of the experiments, their interpretation and relation to the main idea of the study and to the already published works in that field. Also, authors should provide information about implementation of results, potentially new directions for research and conclusions. Authors have to avoid self repetition and copyediting in the text relatively to the abstract and introduction sections.

Figures and Tables, as well as figure legends has to be placed in an appropriate parts of the text and position at the top and bottom of pages and should be assembled into final form (as they will appear in paper). In the figure containing several panels each panel should be labeled as: A, B, C and D. Authors don't need to send figures and tables as separate files additionally to the main text.

Figure captions
should be placed below figures and centered. Use 9pt Times New Roman font for figure and table captions. Figure labels should be legible, about 11pt. The quality of illustrations is of utmost importance. Authors are encouraged to use vector formats for their graphics whenever possible. In the case if a raster format figure has been used, authors should use a proper resolution. The minimum resolution requirements are 600 dpi for line art.

Table captions should be placed above the tables and centered. Leave 0.10 inches space before and after the table caption.

Use 11pt Times New Roman font for Results and Discussion text; 12pt bold Times New Roman font for Results and Discussion heading.

 

Equations. Number equations consequently using Arabic numbers (0, 1, 2, ..., 9). Put equation numbers in parentheses and flush with the right margin, as in (1). Punctuate equations with commas or periods when they are parts of a sentence, as here

                           Ki = IC50/(1 + [S]0/Km)                                (1)

Leave 0.12 inches above and below the equation.

Acknowledgments

Persons who made a contribution to submitted manuscript but were not listed as authors have to be named in acknowledgement section with short description of their contribution.

In the acknowledgement section authors has to put all information about founding sources providing grant numbers or sponsored research agreements, names of organizations and institutions.  Authors should also declare all potential competing interests (if any) related with paper (e.g.: patent applications, products development etc.)

Use 11pt Times New Roman font for Acknowledgements text; 12pt bold Times New Roman font for Acknowledgements heading.

Custom services used in the work

Authors should provide the list of the custom services (if any), which were used in their work, for example:
  • Recombinant protein ABCDEF was produced in Abnova (Walnut, CA, USA)
  • Oligos were synthesized in IDT Inc. (Coralville, IA, USA)
  • DNA cloning, mutagenesis and sequencing of recombinant constructs were done in  Genewiz (South Plainfield, NJ, USA)
  • Custom antibodies GHIJ were produced by AnaSpec Inc. (Fremont, CA,  USA)
  • Peptides synthesis was done by GeneScript USA Inc. (Piscataway, NJ, USA)

Use 11pt Times New Roman font for Custom services used in the work text; 12pt bold Times New Roman font for Custom services used in the work heading.

References

The number of references has to be reasonable and should not exceed 30. In the text of submitted manuscript authors should number citations in square brackets by number only: [1], the numbers have to be placed in order of their appearance in the text; multiple citations have to be in common brackets: [1, 3, 5]; use a hyphen for a range: [2-7].

References should be organized in following manner: author's names, year of publication, title of article, volume number, and page numbers. If referenced paper is accepted, but not published yet - put - in press - instead of volume and page numbers. Use PubMed stile for journal names abbreviations. DOI number (optional) is also acceptable in addition to volume and page numbers.

Use 11pt Times New Roman font for References text; 12pt bold Times New Roman font for References heading.

Some examples are shown below:

[1]  Shikama Y., Yamada M., Miyashita T. (2003) Caspase-8 and caspase-10 activate NF-kappaB through RIP, NIK and IKKalpha kinases. Eur. J. Immunol., 33, 1998-2006.

[2]  Furfine E.S. (2001) HIV protease assays. Curr. Protoc. Pharmacol., Chapter 3: Unit 3.2.

[3]  Docherty A.J., Crabbe T., O'Connell J.P., Groom C.R. (2003) Proteases as drug targets. Biochem Soc Symp., 70, 147-161. Review.

Supplemental materials

            The Journal of Proteolysis Editorial Office strongly believes that it is meaningless for the online journal to have supplemental material section separated from the main manuscript. It means that all figures and tables have to be placed in appropriate parts of the main body of manuscript, but not in supplemental file. Supplemental information may include only extensive data/information that does not fit the regular manuscript page size - e.g., large tables, sequencing information, mass-spectrometry data, microarray data analyses etc. The manuscripts containing inappropriate supplemental materials might be return to authors for correction, which can lead to delay in the manuscript review/publication.

 

 SHORT COMMUNICATIONS Requirements

Manuscript length for short communications should not exceed 3000 words (including figure legends, tables and references), Abstract - 150 words; the number of figures and/or tables - no more than 4 (total); the number of references - up to 20. Each figure should not contain more than 4 panels. If manuscript contains more than 4 figures and/or tables, it will increase the publication fee of manuscript on $100 (USD) per additional figure/table.

Manuscripts should contain sections listed below in the following order:

  • Title (up to 15 words)
  • Authors List
  • Authors Affiliations
  • Abstract (up to 150 words)
  • Introduction
  • Materials and Methods
  • Results and Discussion (with tables, figures and figure legends placed in an appropriate part of the text)
  • Acknowledgments
  • Custom services used in the work (if any)
  • References (up to 20 references)

Detailed descriptions for each section are the same as for REGULAR PAPERS except of special requirements indicated above for manuscript and abstract length, number of figures and tables, and number of references.

REVIEWS Requirements

Manuscript length for review should not exceed 6000 words (including figure legends, tables and references), Abstract - 300 words; the number of figures and/or tables - no more than 8 (total); the number of references - up to 50. Each figure should not contain more than 4 panels. Requirements for references formatting, figures and tables are the same as for REGULAR PAPERS. If review contains more than 8 figures and/or tables, it will increase the publication fee of manuscript on $100 (USD) per additional figure/table.

Reviews should contain sections listed below in the following order:

  • Title (up to 20 words)
  • Authors List
  • Authors Affiliations
  • Abstract (up to 300 words, plus keywords section - up to 5 keywords)
  • Main Text (with tables, figures and figure legends placed in an appropriate part of the text)
  • Acknowledgments
  • References (up to 50 references)

RESUBMISSION Requirements

In the case if corresponding author receives the invitation to resubmit a revised manuscript to the Journal of Proteolysis, he/she needs to provide a new cover letter step by step describing all answers on reviewer's critics and changes that were made in the text. The cover letter for resubmitting manuscripts should be uploaded in Coments to Editor section at the time of revised manuscript submitting process. Also, authors have to upload new version of revised manuscript with incorporated changes.

 

Submission Preparation Checklist

As part of the submission process, authors are required to check off their submission's compliance with all of the following items, and submissions may be returned to authors that do not adhere to these guidelines.

  1. The submission has not been previously published, nor is it before another journal for consideration (or an explanation has been provided in Comments to the Editor in the Cover Letter).
  2. The Journal of Proteolysis accepts submissions via its own electronic submission management system. Articles must be submitted in one of the following formats: MS Word (preferable), Open Office, PDF, RTF or LaTeX. The file extension must indicate the text format (e.g., .pdf, .doc, .docx or .tex).
  3. For the manuscript submission authors should send COVER LETTER and MANUSCRIPT (with included figures, figure legends and tables). All illustrations, figures, and tables should be placed within the text at the appropriate points, rather than at the end.
    The cover letter should be uploaded in Coments to Editor section.
  4. The paper size should be standard US letter (8.5-by-11-inch), 1 inch - left and right margins. The text of manuscript is single-spaced in single-column format; use 12pt Times New Roman font for the body text with the fixed line spacing of 0.19 inches. First paragraph is not first line intended. Use 0.12 inches first line intend for all other paragraphs in a section. For figures and tables Arial and Courier New fonts are allowed. Use italics, rather than underlining (except with URL addresses).  Margins of the text have to be: top - 0.5 inches, bottom - 1 inch, side - 1 inch. Page text area width is 6.5 inches. Page text area height is 8.5 inches including footnotes and figures.
  5. The text adheres to the stylistic and bibliographic requirements outlined in the Author Guidelines, which is found in About the Journal.
  6. The relevant data (e.g. crystal structure data, sequencing data, etc.) have to be deposited in corresponding public databases prior manuscript submission.
  7. Authors of the Journal of Proteolysis do not need to send presubmission letter.
 

Copyright Notice

Manuscripts submitted to the Journal of Proteolysis must represent the original work and has not been previously published and/or is not under consideration for publication elsewhere. The copyright to the article is transferred to the Journal of Proteolysis effective if and when the article is accepted for publication. The corresponding author signs and accepts responsibility for releasing this material on behalf of any and all co-authors. The copyright transfer covers the exclusive right to reproduce and distribute the paper, including reprints, translations, photographic reproductions, microform, electronic form (offline, online) or any other reproductions of similar nature. The Journal of Proteolysis allows unlimited reproduction and distribution of accepted and published papers in which at least one author is U.S. government employee.

The corresponding author guarantees that the manuscript will not be published elsewhere in any language without the consent of the copyright owners, that the rights of third parties will not be violated, and that the publisher will not be legally responsible for any claims for compensation. If authors wishing to include figures or text passages that have already been published elsewhere, they are required to obtain permission from the copyright owner(s) and to include evidence that such permission has been granted when they are submitting their papers. Any material received without such evidence will be assumed as original materials from the authors. In the case when editors of the Journal of Proteolysis will get information and evidences of publication without approval of all authors, republication of already published data, figures or figure manipulations – it will lead to rejection of manuscript without review or to the paper retraction from the journal if it was already accepted and published.

The corresponding author may request from the publisher permission to post an author-created version of the author's paper on his/her own website and his/her institutions repository, including his/her final version: however he/she may not use the publisher's PDF version which is posted on www.jproteolysis.com. Furthermore, the author may only post his/her version of paper if a link is inserted to the original source of publication on Journal of Proteolysis website. The link must be accompanied by the following text: ''The original publication is available at www.jproteolysis.com ''. The author accepts that the publisher reserves the right to refuse posting requests.

 

Privacy Statement

The Journal of Proteolysis provides an Open Access publishing option for authors for publication their original works in all fields of proteolysis and proteolytic pathways. All articles are free to download and authors retain the right to use their article for non-commercial purposes.

This Privacy Policy describes how your personal information is handled for the services on the Journal of Proteolysis websites. It applies generally to the www.jproteolysis.com website and content and other related websites where this policy appears in the footer of the page. The policy that appears in the footer of the page is always the policy that applies. Subject to the requirements of applicable law, the Journal of Proteolysis strives to provide a consistent set of privacy practices. By accepting the Privacy Policy and the User Agreement in registration, you expressly consent to the Journal of Proteolysis’s collection, storage, use and disclosure of your personal information as described in this Privacy Policy. This Privacy Policy is effective upon acceptance for new users and is otherwise effective on December 1, 2013.

You can browse the Journal of Proteolysis’s sites without revealing any personal information about yourself. Once you provide the Journal of Proteolysis with your personal information, for example, once you register as a new user, you are not anonymous to the Journal of Proteolysis. If you choose to give the Journal of Proteolysis your personal information, you consent to the transfer and storage of that information on the Journal of Proteolysis’s servers located in the United States.

The Journal of Proteolysis may collect and store the following personal information: name, email address, physical contact information, professional information, such as research or review interests or biographical information, and (depending on the service used) sometimes financial information, such as credit card or bank account numbers; transactional information based on your activities on the sites (such as submitting, reviewing, discussing, commenting); shipping, billing and other information you provide to purchase a paper or a subscription; community discussions, chats, dispute resolution, correspondence through our sites, and correspondence sent to us; other information from your interaction with the Journal of Proteolysis’s sites, services, content and advertising, including computer and connection information, statistics on page views, traffic to and from the sites, ad data, IP address and standard web log information; additional information the Journal of Proteolysis may ask you to submit to authenticate yourself; information from other companies, such as demographic and navigation data; and other supplemental information from third parties.

The Journal of Proteolysis does not sell or rent your personal information to third parties for their marketing purposes without your explicit consent. The Journal of Proteolysis may combine your information with information collected from other companies and use it to improve and personalize the services, content and advertising. If you do not wish to receive marketing communications from The Journal of Proteolysis or participate in The Journal of Proteolysis’s ad-customization programs, simply indicate your preference in the Journal of Proteolysis or by following the directions provided with the communication or advertisement.

The Journal of Proteolysis’s primary purpose in collecting personal information is to provide you with a safe, efficient, and customized experience. You agree that the Journal of Proteolysis may use your personal information to: provide the services and customer support you request; resolve disputes, collect fees, and troubleshoot problems; prevent potentially prohibited or illegal activities, and enforce our User Agreement; customize, measure and improve the services, content and advertising; tell you about the services, targeted marketing, service updates; and compare information for accuracy, and verify it with third parties.

The Journal of Proteolysis may disclose personal information to respond to legal requirements, enforce the Journal of Proteolysis’s policies, respond to claims that a submission or other content violates the rights of others, or protect anyone's rights, property, or safety. Such information will be disclosed in accordance with applicable laws and regulations. The Journal of Proteolysis may also share your personal information with: members of the www.jproteolysis.com corporate family to provide joint content and services (like registration, transactions and customer support), to help detect and prevent potentially illegal acts and violations of the Journal of Proteolysis’s policies, and to guide decisions about their products, services and communications; service providers under contract who help with the Journal of Proteolysis’s business operations (such as fraud investigations and bill collection); other third parties to whom you explicitly ask us to send your information (or about whom you are otherwise explicitly notified and consent to when using a specific service); law enforcement or other governmental officials, in response to a verified request relating to a criminal investigation or alleged illegal activity, the Journal of Proteolysis in its sole discretion believes necessary or appropriate in connection with an investigation of fraud, intellectual property infringement, piracy, or other unlawful activity; and other business entities, should the Journal of Proteolysis plan to merge with or be acquired by that business entity. Without limiting the above, in an effort to respect your privacy and the Journal of Proteolysis’s ability to keep the community free from bad actors, the Journal of Proteolysis will not otherwise disclose your personal information to law enforcement, other government officials, or other third parties without a subpoena, court order or substantially similar legal procedure, except when the Journal of Proteolysis believes in good faith that the disclosure of information is necessary to prevent imminent physical harm or financial loss or to report suspected illegal activity.

Your User ID is displayed throughout the Journal of Proteolysis (and hence available to the public), and is connected to all of your the Journal of Proteolysis activity. Other people can see your submissions, reviews, discussions, feedback, ratings and associated comments. Notices sent to other community members about suspicious activity and policy violations on the Journal of Proteolysis’s sites refer to User IDs and specific items. If you associate your name with your User ID, the people to whom you have revealed your name will be able to personally identify your jproteolysis.com activities. If you access the Journal of Proteolysis’s sites from a shared computer or a computer in an internet café, certain information about you, such as your User ID, activity or reminders from the Journal of Proteolysis, may also be visible to other individuals who use the computer after you.

The Journal of Proteolysis enables you to share personal information to publish a contribution. The Journal of Proteolysis encourages you to disclose your privacy practices and respect the privacy of other users. The Journal of Proteolysis cannot guarantee the privacy or security of your information. To help protect your privacy, The Journal of Proteolysis allows only limited access to other users' contact information. When users are involved in a review/evaluation of a contribution, they may have access to each other's name, User ID, email address and other contact information. In all cases, you must give other users a chance to remove themselves from your database and a chance to review what information you have collected about them.

You agree to use user information only for: the Journal of Proteolysis transaction-related purposes that are not unsolicited commercial messages; using services offered through the Journal of Proteolysis, or other purposes that a user expressly chooses.

The Journal of Proteolysis uses small files placed on your hard drive called “cookies” on certain of The Journal of Proteolysis’s pages to help analyze The Journal of Proteolysis’s web page flow; customize The Journal of Proteolysis’s services, content and advertising; and promote trust and safety. The Journal of Proteolysis offers certain features that are available only through the use of cookies. The Journal of Proteolysis uses cookies to help identify you and maintain your signed-in status. Most cookies are “session cookies,” that are automatically deleted from your hard drive at the end of a session. You are always free to decline the Journal of Proteolysis’s cookies if your browser permits, although doing so may interfere with your use of some of The Journal of Proteolysis’s sites or services. You may encounter cookies from third parties on certain pages of the sites that the Journal of Proteolysis does not control.

The Journal of Proteolysis does not tolerate spam. Make sure to set your the Journal of Proteolysis notification preferences so the Journal of Proteolysis communicates to you as you prefer. You are not licensed to add other the Journal of Proteolysis users, even a user who has reviewed an article submitted by you, to your mailing list (email or physical mail) without their express consent. To report the Journal of Proteolysis-related spam or spoof emails to the Journal of Proteolysis, please forward the email to   or  .

You may not use the Journal of Proteolysis’s communication tools to send spam or otherwise send content that would violate our User Agreement. The Journal of Proteolysis automatically scans and may manually filter messages to check for spam, viruses, phishing attacks and other malicious activity or illegal or prohibited content, but the Journal of Proteolysis does not permanently store messages sent through these tools. If you send an email to an email address that is not registered in the Journal of Proteolysis’s community (via Suggest-a-Reviewer or other tools), the Journal of Proteolysis does not permanently store that email or use that email address for any marketing purpose. The Journal of Proteolysis does not rent or sell these email addresses.

Your password is the key to your account. Do not disclose your the Journal of Proteolysis password to anyone. If you do share your password or your personal information with others, remember that you are responsible for all actions taken in the name of your account. If you lose control of your password, you may lose substantial control over your personal information and may be subject to legally binding actions taken on your behalf. Therefore, if your password has been compromised for any reason, you should immediately notify the Journal of Proteolysis and change your password.

You can see, review and change most of your personal information by signing on to the Journal of Proteolysis. Generally, the Journal of Proteolysis will not manually modify your personal information because it is very difficult to verify your identity remotely. You must promptly update your personal information if it changes or is inaccurate. Once you make a public posting like a biographical description, you may not be able to change or remove it. Upon your request, the Journal of Proteolysis will close your account and remove your personal information from view as soon as reasonably possible, based on your account activity and in accordance with applicable law. The Journal of Proteolysis does retain personal information from closed accounts to comply with law, prevent fraud, collect any fees owed, resolve disputes, troubleshoot problems, assist with any investigations, enforce our the Journal of Proteolysis User Agreement, and take other actions otherwise permitted by law.

Your information is stored on the Journal of Proteolysis’s servers located in the United States. The Journal of Proteolysis treats data as an asset that must be protected and use lots of tools (encryption, passwords, physical security, etc.) to protect your personal information against unauthorized access and disclosure. However, third parties may unlawfully intercept or access transmissions or private communications, and other users may abuse or misuse your personal information that they collect from the site. Therefore, although the Journal of Proteolysis works very hard to protect your privacy, the Journal of Proteolysis does not promise, and you should not expect, that your personal information or private communications will always remain private.

Except as otherwise expressly included in this Privacy Policy, this document addresses only the use and disclosure of information the Journal of Proteolysis collects from you. If you disclose your information to others, whether they are authors, reviewers or editors on the Journal of Proteolysis sites or other sites throughout the internet, different rules may apply to their use or disclosure of the information you disclose to them. The Journal of Proteolysis does not control the privacy policies of third parties, and you are subject to the privacy policies of those third parties where applicable.

The Journal of Proteolysis may amend this Privacy Policy at any time by posting the amended terms on this site. All amended terms automatically take effect 30 days after they are initially posted on the site. In addition, the Journal of Proteolysis will notify you through the Journal of Proteolysis Announcements. You may write to us at: Polivirtue LLC. Attn: Legal - Global Privacy Practices, 3251 Holiday Court #500, La Jolla, CA 92037, or e-mail to  .