Who we are
++ Through nonprofit oversight and dedicated fiscal management, OpenMS Inc. + helps ensure OpenMS remains freely available, sustainable, and community-driven. +
++ Contributions are tax-deductible to the extent permitted by law. EIN: 93-3818533. +
+Board of directors
++ OpenMS receives direct funding from organizations that sponsor the project. + See sponsor us for current sponsors and how to support OpenMS financially. +
++ Institutional partners are organizations that support the project by employing people + who contribute to OpenMS as part of their work. + See the research partnerships page for partner + institutions and how to collaborate. +
++ If you have found OpenMS useful in your work, research, or company, please consider + a donation commensurate with your resources. Any amount helps and is used strictly to + support OpenMS open-source software, documentation, and community development. +
++ Give online via our + donation page (Zeffy and Open Collective). +
+Corporate Governance
++ OpenMS Inc. is a U.S. nonprofit corporation under 501(c)(3) + that provides legal and financial infrastructure for the project. +
++ OpenMS Inc. provides legal, financial, and organizational stewardship for the project. +
+Project Governance
++ The Executive Committee is the primary governance body + for the software project. It is composed of core developers and led by an elected Executive Chairperson. +
++ Core developers are trusted maintainers who review contributions, + mentor contributors, and participate in project governance decisions through the Executive Committee. +
++ New core developers are added by majority vote of the Executive Committee. + Core developers may step down voluntarily or be removed for inactivity or Code of Conduct violations by a two-thirds vote. +
+Corporate (Board of Directors)
+Legal entity, nonprofit compliance, financial stewardship.
+Project (Executive Committee)
+Software roadmap, contributor governance, technical/community decisions.
++ This model gives OpenMS institutional stability while preserving independent technical governance by the active maintainer community. +
++ User questions: The best way to get help is to post your question + to a site like + Stack Overflow, + with thousands of users available to answer. We wish we could keep an eye on + these sites, or answer questions directly, but the volume is just a little + overwhelming! +
++ Development issues: For OpenMS development-related matters (e.g. + bug reports), please see Community. +
+Discussion
++ The main forum for longer-form discussions — new features, roadmap changes, + and project-wide decisions. Announcements about releases, developer meetings, + sprints, and conference talks are also made here. +
++ Join the mailing list + · + Search the archive +
++ Please use bottom posting, reply to the list (rather than to another sender), + and do not reply to digests. +
+Development
++ Use the tracker for bug reports, documentation issues (e.g. unclear sections), + and feature requests (e.g. new interpolation methods). +
+ +C++ / OpenMS
++ Documentation for the newest release — all classes, functions, and build + instructions for several operating systems. Includes an introduction to core + data structures and algorithms for new developers. +
++ Browse the docs + · + Developer tutorial +
+Python
++ Documentation on how to use OpenMS in Python. +
+ +Infrastructure
++ OpenMS-lib is a mature and reliable C++ framework for omics based mass spectrometry data analysis. +
+ +Key publications
+A proteomics sample metadata representation for multiomics integration and big data analysis
DIAproteomics: A multifunctional data analysis pipeline for data-independent acquisition proteomics and peptidomics
HLA Ligand Atlas: a benign reference of HLA-presented peptides to improve T-cell-based cancer immunotherapy
Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry
FLASHDeconv: ultrafast, high-quality feature deconvolution for top-down proteomics
Feature-based molecular networking in the GNPS analysis environment
Metabolomics data processing using OpenMS
OpenPepXL: an open-source tool for sensitive identification of cross-linked peptides in XL-MS
Phosphoproteomics of short-term hedgehog signaling in human medulloblastoma cells
SmartPeak automates targeted and quantitative metabolomics data processing
Tracing incorporation of heavy water into proteins for species-specific metabolic activity in complex communities
EPIFANY-A method for efficient high-confidence protein inference
MHCquant: automated and reproducible data analysis for immunopeptidomics
Multi-omics discovery of exome-derived neoantigens in hepatocellular carcinoma
Recommendations for the packaging and containerizing of bioinformatics software
ThermoRawFileParser: modular, scalable, and cross-platform RAW file conversion
Automated SWATH data analysis using targeted extraction of ion chromatograms
BioContainers: an open-source and community-driven framework for software standardization
OpenMS–a platform for reproducible analysis of mass spectrometry data
Targeted feature detection for data-dependent shotgun proteomics
The mzIdentML data standard version 1.2, supporting advances in proteome informatics
A multicenter study benchmarks software tools for label-free proteome quantification
Flexible data analysis pipeline for high-confidence proteogenomics
OpenMS: a flexible open-source software platform for mass spectrometry data analysis
Ten simple rules for taking advantage of Git and GitHub
Efficient visualization of high-throughput targeted proteomics experiments: TAPIR
Fast and efficient XML data access for next-generation mass spectrometry
Retention time prediction improves identification in nontargeted lipidomics approaches
Toward improved peptide feature detection in quantitative proteomics using stable isotope labeling
Workflows for automated downstream data analysis and visualization in large‐scale computational mass spectrometry
Automated label-free quantification of metabolites from liquid chromatography–mass spectrometry data
OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data
qcML: an exchange format for quality control metrics from mass spectrometry experiments
An automated pipeline for high-throughput label-free quantitative proteomics
The mzQuantML data standard for mass spectrometry-based quantitative studies in proteomics
Tools for label-free peptide quantification
TOPPAS: a graphical workflow editor for the analysis of high-throughput proteomics data
The mzIdentML data standard for mass spectrometry-based proteomics results
OpenMS and TOPP: open source software for LC-MS data analysis
Probabilistic consensus scoring improves tandem mass spectrometry peptide identification
Optimal de novo design of MRM experiments for rapid assay development in targeted proteomics
TOPP goes Rapid The OpenMS Proteomics Pipeline in a Grid-Enabled Web Portal
De novo peptide sequencing by tandem MS using complementary CID and electron transfer dissociation
OpenMS and TOPP: open source software for LC-MS data analysis
SILACAnalyzer-a tool for differential quantitation of stable isotope derived data
Analysis of mass spectrometric data: peak picking and map alignment
Computational quantification of peptides from LC-MS data
Critical assessment of alignment procedures for LC-MS proteomics and metabolomics measurements
LC-MSsim–a simulation software for liquid chromatography mass spectrometry data
OpenMS–an open-source software framework for mass spectrometry
A fast and accurate algorithm for the quantification of peptides from mass spectrometry data
A geometric approach for the alignment of liquid chromatography—mass spectrometry data
TOPP The OpenMS Proteomics Pipeline
Absolute quantification of myoglobin content in blood serum using HPLC/MS through automatic bioinformatics analysis
Algorithms for the automated absolute quantification of diagnostic markers in complex proteomics samples
OPENMS; a generic open source framework for chromatography/MS-based proteomics
OpenMS-Software for Mass Spectrometry
Visualization
++ Visualization library for mass spectrometry data. Create interactive and static plots + directly from Python dataframes—with matplotlib, Bokeh, and Plotly backends. +
+ +Overview
++ pyopenms_viz extends pandas DataFrames with plot types for spectra, chromatograms, + peak maps, and mobilograms—so you can explore results without building charts from scratch. +
+Plot spectra and chromatograms from long-format DataFrames.
+ Read tutorial +Install with pip install pyopenms-viz.
+ View on PyPI +BSD-licensed source code and issue tracker.
+ View repository +Pair pyopenms_viz with pyOpenMS for end-to-end Python workflows.
+ Explore pyOpenMS +Python
++ Python bindings to OpenMS-lib. Write custom analysis scripts and integrate OpenMS + into Python workflows. +
+Institutional partners
++ Institutional partners are organizations that support OpenMS by employing people + who develop, maintain, and apply the software as part of their research missions. +
+Collaboration
++ Partnerships take many forms—from funded software engineering to joint methods + papers and training for your lab or facility. +
++ The groups below employ contributors who advance OpenMS as part of their research. + Logos link to partner home pages where available. +
+ {{< partners >}} ++ Tell us about your group, infrastructure needs, or ideas for joint development. + We can help you find the right channel—partnership discussion, sponsorship, or + technical support. +
+Impact
++ OpenMS powers proteomics and metabolomics workflows worldwide. Sponsorship helps + the project maintain core libraries, web applications, and training resources + that researchers rely on every day. +
+OpenMS Inc.
++ OpenMS Inc. is a U.S. 501(c)(3) public charity that stewards project finances + and accepts sponsorships aligned with our nonprofit mission. +
++ OpenMS receives direct funding from the organizations below. We are grateful for + their support of open-source mass spectrometry software. +
+ {{< sponsors >}} ++ Whether you represent a company, institute, or foundation, we would like to hear + about your goals and how sponsorship can support OpenMS development and the + broader community. +
+Framework
++ Web interface template for OpenMS pipelines. Deploy custom analysis tools as interactive + web apps without frontend development—built on Streamlit with workspace management, + parameter widgets, and parallel TOPP execution. +
+ +Overview
++ OpenMS WebApps provides an opinionated template for wrapping pyOpenMS and TOPP workflows + in a user-friendly interface. Scientists can test workflows online or download packaged + builds for local deployment. +
+Fork and customize the base app for your OpenMS workflow.
+ View on GitHub +Host multiple WebApps together with Docker Compose.
+ Deployment guide +Community apps built on the OpenMS WebApps framework.
+ Browse applications +OpenMS WebApps: Building User-Friendly Solutions for MS Analysis.
+ Read the paper +
+```
+
+## Tips
+
+- Prefer **PNG** or **SVG** for logos; **JPEG** for photos.
+- Keep file sizes reasonable (compress large screenshots).
+- Use descriptive **alt text** in Markdown/HTML for accessibility.
+- Use lowercase filenames to avoid case-sensitivity issues on Linux (production builds).
+
+## Adding via GitHub
+
+1. In your branch, go to the target folder under `static/images/`.
+2. **Add file** → upload image.
+3. Reference `/images/...` in the same PR.
+
+## Preview
+
+Open the image URL directly: `http://localhost:1313/images/webapp/logo/my-tool.png`
diff --git a/docs/common-tasks/add-news-post.md b/docs/common-tasks/add-news-post.md
new file mode 100644
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+++ b/docs/common-tasks/add-news-post.md
@@ -0,0 +1,108 @@
+# Add a news post
+
+News articles appear on **https://openms.de/news/** and in the news listing. Each post is one Markdown file.
+
+## Files to edit
+
+| Action | Location |
+|--------|----------|
+| New post | `content/en/news/+ The Zeffy donation form will be embedded on this page soon. Until then, + please use Open Collective below or contact us if you need another way to give. +
++ You can also support OpenMS through our + Open Collective + account—useful for recurring community contributions and transparency. +
+{{ . }}
+ {{- end }} + + Learn more + +