Frequently Asked Questions (FAQs) - Journal of Proteome Data and Methods

Data Submission

Authors must submit their own data to publicly repositories, especially Mass Spectrometry data should be submitted to a repository acceding to the ProteomeXchange consortium depending on their data types (see Data Submission Guidelines of ProteomeXchange).

Open Access: What is Open Access?

Open Access is a publishing model in which articles and other materials are made freely available online to be used and reused in specific ways. Anyone with an internet connection can access, download, read, copy, print, store and distribute Open Access publications without restriction. Any use for all licenses must be properly attributed, while other uses, such as re-selling or altering the original for subsequent distribution are sometimes controlled. Open Access increases the accessibility of research output.

There are several forms of Open Access, for example Green, Gold and hybrid. The journal is a Gold Open Access journal. The journal’s policies on deposition to preprint servers and institutional repositories, which facilitate Green Open Access, can be found in the journal’s Instructions to Authors.
How much does it cost to publish articles in the journal?

There are many costs associated with publishing scholarly journals, such as those of managing peer review, copy editing, typesetting, online hosting and allied services such as archiving and support for industry infrastructure. To cover these costs in the absence of revenues such as journal subscriptions, authors (or their institutions or funders) need to pay an Article Processing Charge (APC).

The journal charges an APC ¥150,000 of for all article types. There is a formal waiver policy for authors from developing nations.

IMPORTANT NOTICE: During the launch phase, the journal will be supported by society funds and will be free for authors to publish in and for readers to access regarding all types of manuscripts. Approximately four years after launch (when the initial funding has been exhausted), the journal will instigate an APC.
When and how do I pay the Article Processing Charge?

If your manuscript is accepted, the Editorial Office will send the corresponding author a link to the payment and License to Publish forms, with instructions on how to pay the APC. Your manuscript cannot be published until this payment has been received.
Are there any additional charges?

No. The APC replaces the previous publication charges levied by the journal.
Will Open Access influence the peer review process?

No. The journal’s peer review process remains rigorous and impartial. The Editor’s final decision is based only on the manuscript’s scientific merit and has no bearing on the authors’ ability to pay the APC.
Can I get funding to pay the Article Processing Charge?

Some universities and research institutions provide financial support for researchers’ APCs. Some funding bodies allow grant recipients to use part of their grant money towards Open Access publication costs. Please check with your funding body and/or employer to see if they have systems in place to pay for, or subsidize, APCs.

Please note that the journal Editorial Office will communicate only with the corresponding author regarding the payment of the APC. It is the corresponding author’s responsibility to communicate with any co-authors regarding payment of the APC.

Please also see our waiver policy below.
I can’t pay the Article Processing Charge. Do you have waivers?

The journal will waive the Article Processing Charge for articles where the corresponding author is based in a Research4Life program country. In cases of demonstrated financial hardship, the journal will consider a pre-submission application for a waiver from the corresponding author to jpdm@jhupo.org. Applications cannot be made after the peer review process has started.

The ability of an author to pay the APC does not influence editorial decisions. To avoid any possibility of undue influence, editors involved with the decision-making process for articles are not involved in any deliberations on waivers.
Who owns the copyright in my work?

Authors of all manuscripts retain copyright over their work. The journal publishes articles with a License to Publish from the author under a Creative Commons license.
What licenses does the journal use?

Under the fully Open Access publishing model, the journal offers authors the following Creative Commons licenses: CC BY (Attribution) 4.0 International license.

Further details about the licenses are available in the License to Publish form.

Some funding bodies require articles funded by them to be published under a specific Creative Commons license. Before submitting your work to the journal, check with the relevant funding bodies to ensure that you comply with any mandates.
What rights do I have with respect to my publications?

As the copyright holder, you and your co-authors retain copyright in your article. Note that you assign the journal an irrevocable right to publish, sell, download, read, copy, print, store and distribute your article, and you must provide full attribution to the journal when you publish or derive material from the article.
What rights do others have with respect to my publications?

What others can do with your publication depends on the Creative Commons license under which it is published, however all are valid worldwide and are irrevocable – they remain in place as long as the applicable copyright. 

In the case of the CC BY license, others may distribute, remix, tweak, and build upon your work, even commercially, as long as they credit you and include the journal reference for it.

Further details can be found in the License to Publish form.
Does publishing Open Access mean my manuscript is compliant with my funding body requirements?

The journal’s Open Access policies are compliant with the public access requirements of many major funding bodies worldwide. However, please ensure that you are compliant with your funding body’s or employer’s requirements.