Call for Papers: Software Tools and Resources Part 5

The Journal of Proteome Research is welcoming submissions for its Fifth Biennial Special Issue on Software Tools and Resources.

Software tools and data resources are essential to research in all omics domains, including proteomics and metabolomics. The goal of this recurring Special Issue is to highlight the latest novel and significantly updated software tools, web applications, and databases that scientists can use for data analysis and visualization in proteomics and related research.

For readers, this provides an easily identifiable source of tools specifically reviewed for their applicability and ease of adoption. For authors, this provides increased visibility and wider adoption of their tools within the proteomics community through dissemination and documentation.

For inclusion in this Special Issue, authors must present either a complete description of a relevant novel tool, library, web application, or database (article) or a substantial and meaningful update of a previously published tool or resource (technical note). The full working tool or database must be available free-of-charge to editors and reviewers for evaluation at the time of manuscript submission.

Tools with a graphical or web browser interface are preferred, but the editors will also consider well-documented web service APIs or libraries of functional building blocks for custom data analysis pipelines.

The deadline for submissions is November 2, 2026. Submit your manuscript now.

Organizing Editors

Magnus Palmblad, Associate Editor, Journal of Proteome Research
Leiden University Medical Center, Netherlands

Michael Hoopmann, Guest Editor
University of Washington, United States

Veit Schwämmle, Guest Editor
University of Southern Denmark, Denmark

Viktoria Dorfer, Guest Editor
University of Applied Sciences Upper Austria, Austria

Submission Information

We welcome submissions for this Special Issue through November 2, 2026. For more information on submission requirements, please visit the journal’s Author Guidelines page.

Accepted manuscripts for consideration in this Special Issue will include articles and technical notes. Papers accepted for publication for this Special Issue will be available ASAP (as soon as publishable) online. After all submissions have been published, they will then be compiled online on a dedicated landing page to form the Special Issue. Manuscripts submitted for consideration will undergo the full rigorous peer review process expected from ACS journals.

Open Access: There are diverse open access options for publications in American Chemical Society journals. Please visit our Open Science Resource Center for more information.

Manuscripts presenting research software should also clearly describe its scientific utility, functionality, and novelty. Authors must provide minimum information about the software, including its name, version and website or repository. The architecture, algorithms, LLM code generation and validation should be explicitly described in the manuscript, and licensing and dependencies at least in the repository. The Journal of Proteome Research emphasizes transparent and reproducible research and strongly recommends that software be made available for free and under a recognized open-source license to facilitate broader reuse, reproducibility, and peer verification. Software should ideally be hosted in a publicly accessible repository such as GitHub, accompanied by documentation, installation and user guidelines, and test data. Authors are recommended to create a stable, citable release of the version described in the manuscript with a persistent identifier, e.g. a DOI or SWHID, archive the software in a long-term service like Zenodo or Software Heritage, and create a CFF or CodeMeta file in the repository. Authors are encouraged to follow community engagement strategies for software maintenance and sustainability into the manuscript, following good practices for software development, issue tracking, version control and testing, to enhance scientific reproducibility and impact.

Authors, please:

• Indicate in your cover letter that the manuscript is for the Special Issue on Software Tools and Resources and explain why you consider it suitable for this Special Issue.
• Remember that the full working tool or database must be available free-of-charge to editors and reviewers for evaluation at the time of manuscript submission.
• Be concise and focus the manuscript on the unique or novel functionality of the tool. It should be clear to any reader what problem the system addresses and how it is used.
• For tools and libraries, provide a table to describe the input, operations, and output of each tool. A screenshot of the interface may be included if it has novel or unusual features.

Learn more: See previous editions of our Software and Tools Special Issues from 2019, 2021, 2023, and 2025.

How to Submit

• Log in to the ACS Publishing Center.
• Select the "Journals" tab.
• Choose Journal of Proteome Research.
• Click "Submit."
• Select your manuscript type, and, under "Special Issue Selection," choose “Software Tools and Resources 2027."

If you have any general questions regarding submission to this Special Issue, please contact palmblad-office@jpr.acs.org.