On this pageOops! You’ve reached a dead end.
+If you think something should be here, you can open an issue on GitHub.
+ +About us
+OpenMS Inc. is the corporate entity and fiscal home of the OpenMS project. As a Pennsylvania-based 501(c)(3) public charity, it supports development, governance, and long-term stewardship of the OpenMS ecosystem.
+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. Sponsors include:
+
+
++ Interested in sponsoring us? Contact us for more information. +
+With Open Science, both industry and community profit
OpenMS is building and maintaining a unified, trusted, and openly accessible commons of knowledge, software, education, and research resources for the mass spectrometry community.
As a nonprofit organization, sponsorship contributions are tax-deductible to the extent permitted by law.
Platinum
+$250,000 annually
+Shaping the future of Open Science
For organizations committed to shaping the future of open scientific infrastructure.
Gold
+$50,000 annually
+Strategic investor in Open Science
Strategic investment in open scientific infrastructure.
Silver
+$10,000 annually
+Strong Supporter of Open Science
Strong support for OpenMS training, outreach, and community programs.
Directly support training programs, workshops, and research initiatives.
+Bronze
+$5,000 annually
+Supporter of Open Science
Public recognition for organizations supporting the OpenMS ecosystem.
+ Interested in sponsoring us? Contact us for more information. +
+ 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). +
+Community
+Upcoming OpenMS meetings, workshops, and community outreach worldwide.
+ +Students collaborate with mentors on OpenMS features, documentation, and tool integrations.
+ + +Drop-in session for workflow questions, troubleshooting, and getting started as a contributor.
+ + +Hands-on training on proteomics and metabolomics workflows with OpenMS and TOPP tools.
+ + +Annual developer meeting with tutorials, talks, and code sprints.
+ + ++ 3 + events +
+One-day workshop on MS analysis with OpenMS and OpenDIAKiosk.
+ + +Annual developer meeting with talks, tutorials, and code sprints.
+ + +Four two-day workshops on metabolomics and proteomics for plant biotechnology.
+ + ++ Events are maintained in + data/community_events.yaml + on GitHub. Add or edit entries via pull request—see + how to update events. +
+On this pageJulianus Pfeuffer, Chris Bielow, Samuel Wein, Kyowon Jeong, Eugen Netz, Axel Walter, Oliver Alka, Lars Nilse, Pasquale Domenico Colaianni, Douglas McCloskey, Jihyung Kim, George Rosenberger, Leon Bichmann, Mathias Walzer, Johannes Veit, Bertrand Boudaud, Matthias Bernt, Nikolaos Patikas, Matteo Pilz, Michał Piotr Startek, Svetlana Kutuzova, Lukas Heumos, Joshua Charkow, Justin Cyril Sing, Ayesha Feroz, Arslan Siraj, Hendrik Weisser, Tjeerd M. H. Dijkstra, Yasset Perez-Riverol, Hannes Röst, Oliver Kohlbacher and Timo Sachsenberg
+In BibTeX format:
+@article{pfeuffer2024openms,
+ title={OpenMS 3 enables reproducible analysis of large-scale mass spectrometry data},
+ author={Pfeuffer, Julianus and Bielow, Chris and Wein, Samuel and Jeong, Kyowon and Netz, Eugen and Walter, Axel and Alka, Oliver and Nilse, Lars and Colaianni, Pasquale Domenico and McCloskey, Douglas and others},
+ journal={Nature methods},
+ volume={21},
+ number={3},
+ pages={365--367},
+ year={2024},
+ publisher={Nature Publishing Group US New York}
+}
+Röst, H.L., Sachsenberg, T., Aiche, S., Bielow, C., Weisser, H., Aicheler, F., Andreotti, S., Ehrlich, H.-C., Gutenbrunner, P., Kenar, E., Liang, X., Nahnsen, S., Nilse, L., Pfeuffer, J., Rosenberger, G., Rurik, M., Schmitt, U., Veit, J., Walzer, M., Wojnar, D., Wolski, W.E., Schilling, O., Choudhary, J.S., Malmström, L., Aebersold, R., Reinert, K., Kohlbacher, O.
+In BibTeX format:
+@article{rost2016openms,
+ title={OpenMS: a flexible open-source software platform for mass spectrometry data analysis},
+ author={R{"o}st, Hannes L and Sachsenberg, Timo and Aiche, Stephan and Bielow, Chris and Weisser, Hendrik and Aicheler, Fabian and Andreotti, Sandro and Ehrlich, Hans-Christian and Gutenbrunner, Petra and Kenar, Erhan and others},
+ journal={Nature methods},
+ volume={13},
+ number={9},
+ pages={741--748},
+ year={2016},
+ publisher={Nature Publishing Group}
+}
+We are dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. By participating in this community, participants accept to abide by OpenMS' Code of Conduct and accept the procedures by which any Code of Conduct incidents are resolved. Any form of behaviour to exclude, intimidate, or cause discomfort is a violation of the Code of Conduct.
+OpenMS is a community-led project. We value the involvement of everyone in the community. We are committed to creating a friendly and respectful place for learning, teaching and contributing. All participants in our events and communications are expected to show respect and courtesy to others.
+To make clear what is expected, everyone participating in OpenMS activities is required to conform to the Code of Conduct. This Code of Conduct applies to all spaces managed by OpenMS including, but not limited to, workshops, email lists, and online forums such as GitHub, Discord and LinkedIn. Workshop hosts are expected to assist with the enforcement of the Code of Conduct.
+The OpenMS Code of Conduct Committee is responsible for enforcing the Code of Conduct. It can be contacted by emailing open-ms-c_o_c@lists.sourceforge.net. All reports will be reviewed by the Code of Conduct Committee and will be kept confidential. See the report handling manual for how reports are followed up.
+OpenMS is dedicated to providing a welcoming and supportive environment for all people, regardless of background or identity. As such, we do not tolerate behaviour that is disrespectful to our teachers or learners or that excludes, intimidates, or causes discomfort to others. We do not tolerate discrimination or harassment based on characteristics that include, but are not limited to, gender identity and expression, sexual orientation, disability, physical appearance, body size, citizenship, nationality, ethnic or social origin, pregnancy, familial status, veteran status, genetic information, religion or belief (or lack thereof), membership of a national minority, property, age, education, socio-economic status, technical choices, and experience level.
+Everyone who participates in OpenMS activities is required to conform to this Code of Conduct. It applies to all spaces managed by OpenMS including, but not limited to, workshops, email lists, and online forums such as GitHub, Discord and LinkedIn. Workshop hosts are expected to assist with the enforcement of the Code of Conduct. By participating, participants indicate their acceptance of the procedures by which OpenMS resolves any Code of Conduct incidents, which may include storage and processing of their personal information.
+All participants in our events and communications are expected to show respect and courtesy to others. All interactions should be professional regardless of platform: either online or in-person. In order to foster a positive and professional learning environment we encourage the following kinds of behaviours in all OpenMS events and platforms:
+Note: See the four social rules for further recommendations.
+Examples of unacceptable behaviour by participants at any OpenMS event/platform include:
+Participants who are asked to stop any inappropriate behaviour are expected to comply immediately. This applies to any OpenMS events and platforms, either online or in-person. If a participant engages in behaviour that violates this code of conduct, the organisers may warn the offender, ask them to leave the event or platform (without refund), or engage OpenMS Code of Conduct Committee to investigate the Code of Conduct violation and impose appropriate sanctions.
+This section summarizes the most important points; more details are in the OpenMS Code of Conduct — How to follow up on a report.
+We will investigate and respond to all complaints. The OpenMS Code of Conduct Committee and the OpenMS Executive Committee (if involved) will protect the identity of the reporter, and treat the content of complaints as confidential (unless the reporter agrees otherwise).
+In case of severe and obvious breaches, e.g. personal threat or violent, sexist or racist language, we will immediately disconnect the originator from OpenMS communication channels; please see the manual for details.
+In cases not involving clear severe and obvious breaches of this Code of Conduct the process for acting on any received Code of Conduct violation report will be:
+The Committee will respond to any report as soon as possible, and at most within 72 hours.
+This document is adapted from guidelines written by the The Carpentries Project, which was itself based on the Django Project and Ada Initiative template and the PyCon 2013 Procedure for Handling Harassment Incidents.
+ + +On this page@OpenMS is an open-source C++ software library for LC-MS data management and analysis with python wrappers, a large modular toolset and workflows for e.g., Galaxy, KNIME and nextflow.
+OpenMS is a community-driven open source project developed by a diverse group of contributors. The OpenMS leadership has made a strong commitment to creating an open, inclusive, and positive community. Please read the OpenMS Code of Conduct for guidance on how to interact with others in a way that makes the community thrive.
+Here’s how to get started:
+
channel.We offer several communication channels to learn, share your knowledge and connect with others within the OpenMS community.
+Discord allows the users to communicate in different channels, publicly as well as privately
+The following repositories can be used:
+In case if you are confused, please ask your query here
+The issue tracker can be used for:
+OpenMS
+Documentation
+ +These lists are the main form of receiving OpenMS-related updates, like new features, changes to the roadmap, and all kinds of project-wide decision making.
+There are two mailing list currently:
+To thrive, the OpenMS project needs your expertise and enthusiasm. Not a coder? Not a problem! There are many ways to contribute to OpenMS.
+If you are interested in becoming a OpenMS contributor (yay!) we recommend checking out our Contribute page.
+ +Contact
+Whether you need help with pipelines, integrations, consulting, or joining the community — reach out and we will point you to the right next step.
+Message
++ Share your question or request — we will route it to the right team. +
+More options
++ Prefer email, community chat, or self-service help? Pick the option that fits. +
+Direct
++ Write to the OpenMS team for technical questions, website feedback, or collaboration inquiries. +
+ webmaster@openms.de +Community
++ Join discussions, report issues, and connect with contributors. +
+ View channels +Support
++ Browse help resources or learn about paid scientific and technical support. +
+ OpenMS help +Give back
++ Help sustain open-source mass spectrometry software, community programs, and long-term development. +
+Community
+Learn how to get involved with code, documentation, outreach, fundraising, and more — whether you are new to OpenMS or a seasoned contributor.
+ +Welcome! The OpenMS project welcomes your expertise and enthusiasm. This guide helps you understand how to get involved, whether you’re writing code, improving documentation, helping with community outreach, or contributing in other ways.
+New to OpenMS? Pick a starting point below.
+Most project discussions take place on GitHub and Discord.
+Used for formal discussions related to the project:
+If you encounter a problem or want to propose an improvement, opening a GitHub issue is usually the best place to start.
+ Open a new issue +For informal discussions and quick questions, join the OpenMS Discord server.
+Important technical decisions should still be recorded on GitHub so they remain searchable for everyone.
+ Join Discord +Our community aspires to treat everyone equally and to value all contributions. We have a Code of Conduct to foster an open and welcoming environment.
+Your choices aren't limited to programming — there are many areas where we need your help.
+You do not need to understand the entire codebase before contributing — many contributors begin with documentation improvements, bug reports, or small fixes.
+Check out the contribute section of the project you are interested in:
+OpenMS's User Guide is undergoing rehabilitation. We're in need of new tutorials, how-to's, and deep-dive explanations, and the site needs restructuring. Opportunities aren't limited to writers — we'd also welcome worked examples, notebooks, and videos. OpenMS-Docs lays out our ideas, and you may have others.
+Help shape the OpenMS website — fix bugs, improve layout, add content, or polish the experience for visitors.
+The source lives on GitHub. Browse open issues for ideas, or propose your own.
+For content-only updates without front-end experience, see the website maintainer guide.
+ + + Edit this page on GitHub + +We can barely begin to list the contributions a graphic designer can make here. Our docs are parched for illustration; our growing website craves images — opportunities abound.
+Through community contact we share our work more widely and learn where we're falling short. We're eager to get more people involved in efforts like our Discord server, LinkedIn, BlueSky, and X account, organizing events, a newsletter, and perhaps a blog. To get involved, reach out to communitymanager@openms.de.
+OpenMS was all-volunteer for many years, but as its importance grew it became clear that to ensure stability and growth we'd need financial support. Like all the nonprofit world, we're constantly searching for grants, sponsorships, and other kinds of support. We have a number of ideas and of course we welcome more. Fundraising is a scarce skill here — we'd appreciate your help.
+On this pageWe are an international team on a mission to support scientific and research +communities worldwide by building quality, open-source software. +Join us!
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+ For information about the Executive Committee, please see the Executive Committee page.
+ +On this pageCore developers are trusted contributors who play a central role in maintaining and guiding the OpenMS project. They are active participants in the development of the software and the governance of the project.
+Core developers collectively form the Executive Committee, which is responsible for the long-term direction and governance of OpenMS.
+Core developers serve as maintainers and technical leaders within the project. Their role is to help ensure the quality, sustainability, and collaborative spirit of OpenMS.
+Core developers typically:
+Core developers are expected to contribute to the health of the project in several ways.
+Core developers review pull requests and help maintain code quality across the project.
+Reviews should aim to:
+Core developers help foster a welcoming and collaborative community by:
+Core developers participate in project governance through the Executive Committee. This includes:
+Core developers typically have permission to merge pull requests into the project repositories.
+To maintain code quality and transparency, the project follows these norms:
+These practices help ensure that important changes receive adequate oversight.
+Core developers are individuals who have demonstrated sustained, high-quality contributions to the project and a strong commitment to the OpenMS community.
+Typical characteristics include:
+New core developers are added by a majority vote of a quorum of the Executive Committee, as defined in the project bylaws.
+Core developers are expected to remain active participants in the project.
+Activity may include:
+Members who become inactive for extended periods may be removed by a vote of the Executive Committee as described in the bylaws.
+The OpenMS project values transparency in its governance.
+Core developers participate in Executive Committee meetings where project governance and major decisions are discussed. Minutes from these meetings are recorded and made publicly available unless the committee decides otherwise.
+Coming soon
+This list is maintained by the Executive Committee and updated as membership changes.
+For guidance on getting started as a contributor, see the Contributing Guide.
+ +Community
+Annual Developer Retreat
+The OpenMS annual developers retreat brings together researchers worldwide to shape the future of open-source computational mass spectrometry. It is targeted to core developers, new developers, and potential future contributors of OpenMS projects and apps. Short talks, developer tutorials, and code sprints will be intertwined. Participants will have the opportunity to design custom tools and workflows together with instructors. This retreat provides a great opportunity to get involved with the OpenMS community.
+ Support OpenMS
+Your gift helps sustain open-source mass spectrometry software, documentation, and community programs.
++ If OpenMS has been useful in your research, teaching, or company work, please consider + a donation commensurate with your resources. Gifts are used strictly to support + OpenMS open-source software, documentation, and community development. +
+OpenMS Inc. is a U.S. 501(c)(3) public charity. Donations may be tax-deductible for U.S. donors where permitted by law.
++ We process donations through + Zeffy, + a zero-fee platform for registered nonprofits—so your contribution goes further. +
+ 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. +
+On this pageThe Executive Committee is the primary governance body of the OpenMS project. It is responsible for guiding the technical direction, long-term sustainability, and community governance of OpenMS.
+The committee is composed of the core developers of the project and is led by an Executive Chairperson elected from among its members.
+The Executive Committee provides leadership for the OpenMS project by:
+The Executive Committee is responsible for:
+The Executive Committee consists of the core developers of OpenMS.
+Core developers are individuals who are active and key participants in the project and who help maintain the software, guide development, and support the community.
+New core developers may be added by a simple majority vote of a quorum of the Executive Committee.
+Core developers may be removed due to inactivity or violation of the Code of Conduct by a two-thirds majority vote of a quorum of the Executive Committee, or by request of the member.
+The Executive Committee elects an Executive Chairperson from among its members for a one-year term.
+The responsibilities of the Executive Chairperson include:
+The Executive Chairperson may be removed by a two-thirds vote of the Executive Committee.
+The Executive Committee meets regularly to coordinate the governance and development of the project.
+Meeting rules:
+Any member of the Executive Committee may propose amendments to the project bylaws.
+The amendment process:
+In keeping with the principles of open science and open-source collaboration:
+This commitment ensures transparency and accountability in the governance of the OpenMS project.
+For guidance on getting started as a contributor, see the Contributing Guide.
+ +Community
+Work alongside researchers worldwide in building and testing our projects. Contributions can range from developing algorithms, testing software or writing tutorials. This is a fully remote, unpaid fellowship requiring biweekly mentor meetings. Successful candidates receive a certificate of completion.
+ Complete the application below. We review submissions on a rolling basis and will follow up by email. +
+Fellows are matched with a mentor on one of these OpenMS ecosystem projects. Browse each project to learn more and see how to contribute.
Core C++ library and TOPP tools for LC-MS data management and analysis.
+ +Python bindings for scripting, notebooks, and workflow integration.
+ +Visualization library for spectra and chromatograms from pandas dataframes.
+ +Streamlit-based web applications built on OpenMS pipelines.
+ +User guides, tutorials, and developer documentation for the OpenMS ecosystem.
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+ On this pageThe source code of the OpenMS library as well as the TOPP tools and TOPPView are hosted on GitHub. The most important repositories for starting developers will be OpenMS itself and its contrib (i.e. its dependencies). The source code is released under a three-clause BSD license.
+A good starting point for developers is the OpenMS GitHub wiki. For a quick dive into developing your own, see the Developer FAQ and the Adding your own tool to the TOPP suite.
+The full official OpenMS/TOPP documentation can be found:
+If you want to develop your own OpenMS tool with C++, you will profit on the use of OpenMS’ own:
+For more information, take a look at our Developer FAQ, especially the TOPP section, and the OpenMS C++ guide. Be sure to also check out our OpenMS style guide.
+pyOpenMS are the Python bindings to the OpenMS library which are available for Windows, Linux and OSX.
+The pyOpenMS package contains Python bindings for a large part of the OpenMS library for mass spectrometry based proteomics. It thus provides providing facile access to a feature-rich, open-source algorithm library for mass-spectrometry based proteomics analysis. These Python bindings allow raw access to the data-structures and algorithms implemented in OpenMS, specifically those for file access (mzXML, mzML, TraML, mzIdentML among others), basic signal processing (smoothing, filtering, de-isotoping and peak-picking) and complex data analysis (including label-free, SILAC, iTRAQ and SWATH analysis tools).
+After importing pyOpenMS in your python tool, you can use the python bindings of almost all OpenMS classes. This means you can use methods and classes as they would be python methods or classes. You can access the stored values in objects using the provided functions of the respective class.
+Calling methods from pyOpenMS objects works just as with other python objects. The pyOpenMS bindings ensure that C++ types that are mappable are being mapped to their python ‘equivalent’. This means that you can e.g. use your data, already in python lists as input to a OpenMS class object function (i.e. often either an accessor or algorithm implementation) or the output of such to further process the data in your python code.
+For further help, please also consult the extensive pyOpenMS Documentation.
+ +On this pageThe source code of the OpenMS library as well as the TOPP tools and TOPPView are hosted on GitHub. The most important repositories for starting developers will be OpenMS itself and its contrib (i.e. its dependencies). The source code is released under a three-clause BSD license.
+A good starting point for developers is the OpenMS GitHub wiki. For a quick dive into developing your own, see the Developer FAQ and the Adding your own tool to the TOPP suite.
OpenMS governance
+OpenMS combines a nonprofit corporation for legal and financial stewardship with an Executive Committee that leads technical direction and community governance.
+ +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. +
+On this pageSupport
+Find the right channel for user questions, development issues, documentation, and community discussion — from Stack Overflow to the OpenMS mailing list.
+ ++ 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. +
+ +On this pageOpenMS Inc. LLC
+502 W 7th ST, STE 100
+Erie, PA 16502 USA
+
+Contact:
Expert-crafted ecosystem of computational mass spectrometry tools. Run scientifically vetted, cutting edge apps. Build custom tools on top of robust open-source algorithms. Join the OpenMS community.
+OpenMS
+0+
+Over two decades of open-source development for mass spectrometry workflows.
+0+
+Peer-reviewed research citing OpenMS tools and algorithms worldwide.
+v0
+Continuous releases with new algorithms, formats, and analysis workflows.
+Community tools
+Apps are scientifically validated end-to-end solutions for common proteomics and metabolomics analysis. Test online, then download and deploy locally.
+
+ Web-based analysis and visualization of top-down proteomics data
+ + View app + + +
+ Interactive DIA proteomics data analysis
+ + View app + + +
+ Web-based access to the umetaflow pipeline
+ + View app + + +
+ Web-based workflow for DDA proteomics
+ + View app + + +
+ Web-based access to the nucleic acid search engine (NASE)
+ + View app + + +
+ Web-based analysis pipeline for XL-MS data
+ + View app + + +
+ Web-based analysis pipeline for immunopeptidomics
+ + View app + + +
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+ Reusable C++ algorithms and data structures for mass spectrometry software. Ships with The OpenMS Pipeline (TOPP) command line tools for mass spectrometry analysis.
+ + Learn more + +Python bindings to OpenMS-lib. Write custom analysis scripts and integrate OpenMS into Python workflows.
+ + Learn more + +Web interface template for OpenMS pipelines. Deploy custom analysis tools as interactive web apps without frontend development.
+ + Learn more + +Visualization library for mass spectrometry data. Create interactive and static plots directly from Python dataframes.
+ + Learn more + ++ + Community +
+OpenMS is built by a diverse group of contributors around the world. Whether you are new to mass spectrometry or a seasoned developer, there is a place for you in our community.
+We are teaching a one-day workshop on MS analysis with OpenMS and OpenDIAKiosk at the University of Helsinki on April 30th 2026. Click the header above for more …
+OpenMS announces Maria Llambrich Rodriguez as the 2026 Rising Star in Computational Mass Spectrometry recipient.
+The OpenMS team applies as an organization for GSoC 2026 and invites the computational mass spectrometry community to join us in this effort.
+We are teaching four two-day workshops in February 2026 in South Africa! Click the header above for more information.
+Students collaborate with mentors on OpenMS features, documentation, and tool integrations.
+ + +Drop-in session for workflow questions, troubleshooting, and getting started as a contributor.
+ + +Hands-on training on proteomics and metabolomics workflows with OpenMS and TOPP tools.
+ + +Annual developer meeting with tutorials, talks, and code sprints.
+ + ++ + Contact +
++ Tell us about your pipeline, integrations, or tooling goals — we will point you to the fastest next step. +
+Use the contact form for workflows, integrations, and support questions.
+ + Contact us + + + +Reach us directly at webmaster@openms.de for quick questions or routing help.
+ + webmaster@openms.de + + + +Installation guides, tutorials, and workflow documentation on Read the Docs.
+ + Open docs + + + +On this pageIf you love open science and would like to work within a large research-oriented open-source project feel free to contact us about specific project details.
+In general, you will work in a multidisciplinary Applied Bioinformatics research group as part of the mass-spectrometry special interest group as part of a diverse team of developers and scientists. A large part of the group is located at the WSI for Informatics of the University of Tübingen but associations exist with the clinics and the Max-Planck-Institute.
+On this pageMany of the tools and algorithms provided by OpenMS are developed with both proteomics and metabolomics in mind. First you convert vendor-specific formats into an open community-driven format. You can then filter, centroid, and recalibrate your spectra. OpenMS provides tools that are specifically designed for the metabolite quantification and metabolite identification. All tools are available as nodes in the workflow engine KNIME.
+
+OpenMS provides a large amount of tools to analyse your proteomics datasets. +Starting from input files in either vendor-specific raw formats (convertible with the integrated ProteoWizard) or a number of open HUPO-compliant formats (mzML, mzXML), you can process your data by simply combining a set of our almost 200 ready-made tools from „The OpenMS proteomics pipeline (TOPP)”. These tools are available from the command line and from within workflow engines (e.g. KNIME and Galaxy).
On this pageMany of the tools and algorithms provided by OpenMS are developed with both proteomics and metabolomics in mind. First you convert vendor-specific formats into an open community-driven format. You can then filter, centroid, and recalibrate your spectra. OpenMS provides tools that are specifically designed for the metabolite quantification and metabolite identification. All tools are available as nodes in the workflow engine KNIME.
+On this page
+OpenMS provides a large amount of tools to analyse your proteomics datasets. +Starting from input files in either vendor-specific raw formats (convertible with the integrated ProteoWizard) or a number of open HUPO-compliant formats (mzML, mzXML), you can process your data by simply combining a set of our almost 200 ready-made tools from „The OpenMS proteomics pipeline (TOPP)”. These tools are available from the command line and from within workflow engines (e.g. KNIME and Galaxy).
+These TOPP tools can roughly be categorised based on their applicability to certain common tasks of a proteomics pipeline:
+Import, export and conversion of vendor formats and several open community-driven XML formats (LINK and make a list somewhere)
+Preprocessing of spectra
+MS2 spectrum identification
+Working with MS1 maps
+Protein inference with Fido
+Visualisation of spectra (on all MS levels), features and peptide identifications in our TOPPView
+Finding RNA and protein-protein crosslinks
+Identification of phosphorylation sites with Luciphor
+Support for data independent acquisition via OpenSWATH integration
+A full list of the tools can be found in our documentation here
+If you do not find what you are looking for and you have some experience in developing C++, you can adapt, extend as well as add new tools by contributing to our library or using the library in your own project (see our “Getting Started”).
+ +We want to invite you to the next edition of our online Data and Code Clinic. This is a web-based video help desk for proteomics and metabolomics researchers. We want to help people with their first steps in the exciting and multifaceted field, to facilitate the (sometimes) steep learning curve, and help using advanced data analysis options.
+ +The OpenMS developers meeting brings bioinformaticians working in computational mass spectrometry together to shape the future development of OpenMS. It is targeted to core developers, new developers, and potential future contributors. Short talks, developer tutorials, and code sprints will be intertwined. Participants will have the opportunity to design custom tools and workflows together with instructors. External users are welcome to bring their own ideas and will receive detailed feedback as well as help getting started in OpenMS development. Progress will be tracked on our GitHub page with a resume of each day.
+ +OpenMS · News
+The OpenMS developers meeting brings bioinformaticians working in computational mass spectrometry together to shape the future development of OpenMS. It is targeted to core developers, new developers, and potential future contributors. Short talks, developer tutorials, and code sprints will be intertwined. Participants will have the opportunity to design custom tools and workflows together with instructors. External users are welcome to bring their own ideas and will receive detailed feedback as well as help getting started in OpenMS development. Progress will be tracked on our GitHub page with a resume of each day.
+ +OpenMS · News
+The OpenMS developers meeting brings together people working in computational mass spectrometry to shape the future development of OpenMS. It is targeted to core developers, new developers, and potential future contributors. Short talks, developer tutorials, and code sprints will be intertwined. Participants will have the opportunity to design custom tools and workflows together with instructors. New developers will receive help getting started in OpenMS development. Progress will be tracked on our GitHub page with a resume of each day. For more details ping Tjeerd Dijkstra or Timo Sachsenberg on Gitter.
+ +OpenMS · News
+The OpenMS Deveopers meeting concluded successfully after several days of fruitful discussions and coding sessions. Yasset Perez-Riverol from the EMBL-EBI Proteomics team presented his progress in using Workflows built with OpenMS to reanalyze the accumulated data in the PRIDE database. Members of the KNIME team showed off new features of the upcoming release of the KNIME Analytics Platform Version 5 and received helpful feedback. The OpenMS team discussed the future focus and direction of the project and some coding was done to further the release of OpenMS 3.0. The meeting was rounded off with a one-day visit to the nearby Krka National Park.
+ +OpenMS · News
+The OpenMS developers conference brings together people working in computational mass spectrometry to shape the future development of OpenMS. It is targeted to core developers, new developers, and potential future contributors. Short talks, developer tutorials, and code sprints will be intertwined. Participants will have the opportunity to design custom tools and workflows together with instructors. New developers will receive help getting started in OpenMS development. Progress will be tracked on our GitHub page with a resume of each day. For more details ping Tjeerd Dijkstra or Timo Sachsenberg on discord or by email.
+
+
OpenMS · News
+The OpenMS developers conference brings together people working in computational mass spectrometry to shape the future development of OpenMS. It is targeted to core developers, new developers, and potential future contributors. Short talks, developer tutorials, and code sprints will be intertwined. Participants will have the opportunity to design custom tools and workflows together with instructors. New developers will receive help getting started in OpenMS development. Progress will be tracked on our GitHub page with a resume of each day. For more details ping Tjeerd Dijkstra or Timo Sachsenberg on discord or by email.
+
+Click here for more details and registration
+
+
OpenMS · News
+The OpenMS developers conference brings together people working in computational mass spectrometry to shape the future development of OpenMS. It is targeted to core developers, new developers, and potential future contributors. Short talks, developer tutorials, and code sprints will be intertwined. Participants will have the opportunity to design custom tools and workflows together with instructors. New developers will receive help getting started in OpenMS development. Progress will be tracked on our GitHub page with a resume of each day. For more details ping Tjeerd Dijkstra or Timo Sachsenberg on discord or by email.
+
+Click here for more details and registration
+
+
The OpenMS Fellowship is organized by the Chan Zuckerberg Initiative foundation and the +OpenMS team with the support of Females in Mass Spectrometry (FeMS) society. The +OpenMS fellowship aims to increase diversity within the computational mass spectrometry +field by recruiting scientists from underrepresented backgrounds to join an immersive in- +person mentorship program. Priority will be given to scientists from underrepresented +backgrounds.
+Application open date: 1st April, 2024
+Application close date: 19th April, 2024
+In-person assignment to a computational mass spectrometry lab for 6-weeks
+Applicants are expected to start their 6-week in-person training sometime in in May — July 2024. The exact start date is to be determined in coordination with your host lab.
+Applicants MUST complete in-person training by the end of August 2024.
+Receive $10,000 CAD to cover travel and living expenses while completing in-person +training.
+Link to Application: https://airtable.com/appItu820YKeiWR9g/shrEJaSSS3zIvhlX4
+Application material:
+Applicant must choose one potential host lab to apply to:
+Dr. Laurent Gatto (De Duve Institute UCLouvain, Belgium) +The lab is interested in statistical learning, high throughput biological data, and a notable focus +on single-cell proteomics. The lab actively contribute to the Bioconductor project and prefers R +programming language but open to other languages including Python, Rust, Julia or C/C++.
+For more information, visit: https://lgatto.github.io/cbio-lab/
+Dr. Mathias Wilhelm (Technical University of Munich, Germany) +The lab is interested in deep learning, computational proteomics and big data analysis. The +preferred programming language is Python.
+For more information, visit https://www.mls.ls.tum.de/en/compms/home/
+Dr. Viktoria Dorfer (University of Applied Sciences Upper Austria, Austria) +The lab focuses on the development of algorithms for peptide identification in +bottom-up mass spectrometry data. The preferred programming language is C# +and Python.
+For more information, visit: https://protrein.eu/supervisor/viktoria-dorfer/ and https://bioinformatics.fh-hagenberg.at
+Describe your research motivation and how it aligns with the host lab you have selected +(150 words max).
+How have you and/or will you contribute to advocating and uplifting underrepresented +groups in the field of computational mass spectrometry (100 words max).
+Name one individual to submit a recommendation letter on your behalf. The individual could +be your research advisor, a professor, an employer or anyone that can speak about your +character and research contributions. The individual will receive an email asking them to +upload a letter and will receive a confirmation email after we receive it.
+If you have questions — please email us at edi@openms.org
+The payment of the award to the recipient will be processed through the University of Toronto. +The recipient is expected to sign a letter confirming their acceptance of the award and an +attestation form indicating that the funds have been received. The recipient will have the choice +of receiving funds via wire transfer or by cheque.
+The Chan Zuckerberg Initiative was founded in 2015 to help solve some of society’s toughest +challenges — from eradicating disease and improving education, to addressing needs for our +local communities. Our mission is to build a more inclusive, just, and healthy future for +everyone. +OpenMS offers an open-source C++ library (+ Python binding) for LC-MS data management, +analysis, and visualization. It empowers rapid development of mass spectrometry related +software. OpenMS is freely available under the three clause BSD license and runs under +Windows, MacOS and Linux. The OpenMS members have a strong commitment to creating an +open, inclusive, and positive community in the computational mass spectrometry field.
+
+ 
+
+ 
+
Females in Mass Spectrometry (FeMS) is a community-led initiative to create a network of +support for women in the field of mass spectrometry. Our goal is to bring together, encourage, +empower and facilitate viability of women in mass spectrometry - and to create connectivity +between all members of the mass spectrometry community. +We strive to engage our entire community: women in mass spectrometry and their supporters - +to hear and learn from all perspectives. As a global initiative FeMS support all related events +where women working the MS field gather.
+ +🎉 OpenMS is part of GSoC 2025 – Two Projects Accepted!
+We’re thrilled to announce that two OpenMS projects have been accepted for Google Summer of Code 2025! 🚀
+A big thank you to everyone who took the time to submit a proposal. Your enthusiasm and creativity are what make open-source thrive.
+This year’s GSoC was extremely competitive, with:
We’re proud to be part of this global community, and we’re looking forward to working with our selected contributors on advancing open mass spectrometry software.
+More info: OpenMS GSoC 2025 program page
+ +Google Summer of Code (GSoC) 2026 OpenMS is planning to apply as an umbrella organization and we would like to extend an invitation to other projects and groups within the computational mass spectrometry and proteomics/metabolomics communities to join us in this effort.
+We believe that the primary goal of your participation in GSoC should be learning how to participate in open-source communities. We also believe that it is quite possible to use generative AI to be a more effective participant in our community. Therefore we do not prohibit the responsible use of AI tooling in either your contributions, or your written communications. All AI models were trained on open-source code. We like to think that they can give back a bit to the community as well. This policy comes with a number of major caveats:
+Using an agent effectively can be challenging. Each model has specific ways that they fail, and specific limitations. Learn these before using an agent to build code.
+The skill that an agent has in writing and understanding code is proportional to how much similar code it has seen. In our experience this means that it is much better at solving pandas dataframe formatting issues than esoteric C++ bugs.
+Asking an agent to explain code, or program logic can be a good first step to understanding. OpenMS is a large software project, and trying to unravel how a specific piece of logic works can be daunting. Our team has internally had very good success using agents to speed up learning how a section of code works. Just keep in mind that it can be wrong sometimes.
+Asking the agent for proof is always a good idea.
+Proposed Mentors: OpenMS Team
+Skills: C++, XML Parsing, Mass Spectrometry Imaging
+Estimated Project Length: 350 hours | Difficulty: Medium
Mass spectrometry imaging (MSI) is a powerful analytical technique that enables spatial mapping of molecules in biological tissues. The imzML format is the open standard for storing MSI data, consisting of two files: an XML metadata file and a binary data file. While imzML is widely used in the MSI community, OpenMS currently lacks native support for reading and writing this format.
+The goal of this project is to implement a robust imzML parser in OpenMS, enabling seamless integration of mass spectrometry imaging data into existing OpenMS workflows.
+Tasks:
+Proposed Mentors: OpenMS Team
+Skills: Python, C++, Nanobind, Cython
+Estimated Project Length: 350 hours | Difficulty: Medium to Advanced
PyOpenMS provides Python bindings for OpenMS, enabling Python developers to access the powerful mass spectrometry algorithms implemented in OpenMS. Currently, these bindings are generated using Cython via the autowrap package. While functional, this approach has limitations in terms of maintenance overhead, compile times, and certain Python integration features.
+Nanobind is a modern C++17 library for creating Python bindings with minimal overhead. An existing prototype demonstrates the feasibility of using nanobind for OpenMS Python bindings. This project aims to build upon this prototype to create comprehensive nanobind-based Python bindings for OpenMS.
+A key deliverable of this project is a thorough evaluation comparing nanobind-based bindings against the current autowrap/Cython implementation. This evaluation should cover:
+Tasks:
+Proposed Mentors: Joshua Charkow
+Skills: C++, Algorithm Optimization, Profiling
+Estimated Project Length: 200 hours | Difficulty: Medium
OpenSwathWorkflow is a central component of OpenMS for Data Independent Acquisition (DIA) analysis, enabling targeted extraction and scoring of chromatographic signals using spectral libraries. While OpenSwathWorkflow performs well for conventional experimental libraries, the increasing adoption of large in silico–generated spectral libraries presents substantial computational challenges. Such libraries can contain millions of precursors, leading to increased memory usage, longer runtimes, and scalability bottlenecks in candidate selection and scoring.
+This project aims to analyze and improve the computational performance and scalability of OpenSwathWorkflow, with a particular focus on workflows using very large in silico spectral libraries. The goal is to identify bottlenecks, redesign performance-critical components where necessary, and introduce optimizations that enable efficient processing without compromising identification quality.
+A key deliverable of this project is a systematic performance evaluation of OpenSwathWorkflow before and after optimization.
+Tasks:
+Proposed Mentors: OpenMS Team
+Skills: CMake, Git, Command Line, Linux, macOS, Windows
+Estimated Project Length: 175 hours | Difficulty: Medium
Like many large scale software projects, OpenMS has numerous
+development dependencies. Unfortunately, there is no straightforward
+way to quickly and easily install all of these dependencies. Some can
+be installed using various package managers such as apt-get, brew,
+or choco, while others need to be installed with a Python package
+manager such as conda. And finally, some dependencies need to be
+compiled from source code manually.
The goal of this project is to unify dependency management using the +vcpkg package manager. A successful outcome will be a simplified +developer experience where only a small number of tools are required +in order to set up a full OpenMS development environment. For OpenMS +dependencies that are not available in vcpkg, it will be necessary to +contribute a recipe to the vcpkg community using Git.
+Proposed Mentors: Kyowon Jeong, Tom Müller
+Skills: Python, mass spectrometry, proteomics, data visualization, OpenMS, web development
+Estimated Project Length: about 350 hours | Difficulty: Advanced
Top-down proteomics enables the direct analysis of intact proteoforms, providing unparalleled insight into proteoforms, distinct molecular forms of a protein arising from a single gene, including protein isoforms, truncations, and post-translational modifications. However, interpreting individual spectra and connecting observed masses to biologically meaningful proteoforms remains a major bottleneck. +This project aims to develop an interactive, proteoform-centric visualization and manual analysis tool, inspired by ProSight Lite, to enable rapid interpretation of top-down mass spectrometry data at the single-spectrum level. By integrating advanced visualization with fast targeted searches, the tool will allow researchers to quickly assess truncations, modifications, and mass discrepancies for a given protein of interest. Moreover, it will include feature-level visualization of proteoform ions over m/z-retention time dimension that will allow for quick and accurate validation of proteoform quantification results. +By lowering the barrier between raw spectra and biological interpretation, this project will directly support exploratory proteomics, method development, and hypothesis testing in challenging top-down datasets.
+Project Goals +The student will design and implement an interactive analysis module that enables:
+Proposed Mentors: William Stafford Noble, Wout Bittremieux
+Skills: Python, PyTorch, Deep learning, Profiling
+Estimated Project Length: 350 hours | Difficulty: Advanced
De novo peptide sequencing is a powerful approach for molecular discovery that deciphers peptides directly from tandem mass spectrometry (MS/MS) data. Casanovo is a state-of-the-art AI tool that treats de novo sequencing like a language translation problem—converting sequences of peaks in an MS/MS spectrum into amino acid sequences, just like translating one language into another. Powered by a transformer deep neural network, Casanovo has already revolutionized peptide sequencing, but its inference speed remains a bottleneck.
+In this project, we aim to optimize Casanovo to enable real-time sequencing of spectra as they are produced on the mass spectrometer at a rate of approximately 20–100 Hz. In this setting, we need to achieve both high throughput and low latency.
+A version of Casanovo capable of real-time sequencing will enable the mass spectrometer to make decisions in real time about which types of peptide dissociation techniques to employ or whether to subject a given collection of ions to additional rounds of fragmentation. In so doing, we can use real-time Casanovo to unlock new biological insights at an unprecedented scale. Whether it’s identifying unknown proteins, uncovering disease biomarkers, or advancing drug discovery, your contributions will have a real-world impact on science and healthcare. If you love machine learning, performance optimization, and AI-driven discovery, then this project is your chance to make a difference in computational biology.
+Project Goals:
+This project aims to produce the world’s first real-time de novo sequencer, enabling researchers to make new discoveries and push the boundaries of proteomics research. You will:
The OpenMS team has won a 2021 Google Season of Docs grant to update the OpenMS documentation. From 1 June until 30 September 2021, technical writer Rahul Agrawal will review and rewrite OpenMS documentation, with a focus on pyOpenMS.
+ +The OpenMS team has won a 2022 Google Season of Docs grant to update the OpenMS documentation. Combined with money from the University of Tübingen and from the Chan-Zuckerberg Initiative, a team of three technical writers will review and rewrite OpenMS documentation. The 2022 team consists of Rahul Agrawal, Christina Kumar and Tapasweni Pathak.
+ +The OpenMS team will teach a one-day workshop on mass spectrometry analysis with OpenMS and OpenDIAKiosk at the University of Helsinki.
+
+Topic: MS analysis with OpenMS and OpenDIAKiosk
+
+Educators: Sam Wein and Tom David Müller
+
+Date: April 30th, 9:00-17:00
+
+Location: Sali 3, Biomedicum 1, Meilahti Campus, University of Helsinki
+
+Contents:
+
+This course provides a comprehensive overview of key technologies in mass spectrometry-based proteomics, offering a balanced mix of theoretical lectures and hands-on exercises. Core topics include an introduction to liquid chromatography-tandem mass spectrometry (LC-MS/MS), data-dependent acquisition (DDA), data-independent acquisition (DIA), as well as strategies for accurate protein identification and quantitation.
+
+Learning goals:
+
+Participants will improve their theoretical understanding of mass spectrometry as well as their skills at using OpenMS and other bioinformatics resources to analyze data.
+
+Prerequisites:
+
+Participants should bring laptops to be able to carry out this training on their own computers.
+
+Keywords: Proteomics, Mass spectrometry, Bioinformatics, LC-MS/MS, Data Independent Acquisition
+
+Contact: Sam Wein: sam@openms.de
+
OpenMS
+Announcements, releases, workshops, and community updates from OpenMS.
++ Workshop at University of Helsinki on April 30th 2026. +
+ +We are teaching a one-day workshop on MS analysis with OpenMS and OpenDIAKiosk at the University of Helsinki on April 30th 2026. Click the header above for more information.
+ Read article ++ 2026 Recipient Announced: Rising Star in Computational Mass Spectrometry +
+ +OpenMS announces Maria Llambrich Rodriguez as the 2026 Rising Star in Computational Mass Spectrometry recipient.
+ Read article ++ Google Summer of Code 2026 +
+ +The OpenMS team applies as an organization for GSoC 2026 and invites the computational mass spectrometry community to join us in this effort.
+ Read article ++ OpenMS/CIBI workshops in South Africa from 9 until 20 February 2026. +
+ +We are teaching four two-day workshops in February 2026 in South Africa! Click the header above for more information.
+ Read article ++ OpenMS developers meeting 23-27 March 2026, in Piotrowice Nyskie Palace, Otmuchów, Poland. +
+ +We are hosting the developers meeting near Otmuchów, Poland! Click the header above for more information.
+ Read article +We have just released OpenMS 3.5.0
+ Read article ++ OpenMS Open House November 9th 2025, @10am in Toronto, Canada +
+ +We are organizing an open house in Toronto, Canada! Click the header above for more information.
+ Read article ++ Celebrating 20 years of OpenMS +
+ +We are celebrating 20 years of OpenMS on 1 August 2025 with a BBQ at Sand, Tübingen University. Click the header above for more information.
+ Read article +We have just released OpenMS 3.4.1
+ Read article ++ GSoC 2025 – Two Projects Accepted! +
+ +We’re thrilled to announce that two OpenMS projects have been accepted for Google Summer of Code 2025! 🚀
+ Read article +We have just released OpenMS 3.3 click here to see changes and improvements
+ Read article ++ OpenMS developers meeting 17-21 March 2025, in Xewkija, Gozo, Malta +
+ +We are hosting a developers meeting near Xewkija, Gozo, Malta! Click the header above for more information.
+ Read article +We have just release OpenMS 3.2 click here to see changes and improvements
+ Read article ++ OpenMS Users Meeting 17-18 October 2024, in Berlin, Germany +
+ +We are organizing a users meeting in Berlin, Germany! Click the header above for more information.
+ Read article ++ OpenMS Summer 2024 Fellowship Application +
+ +The OpenMS fellowship aims to increase diversity within the computational mass spectrometry field by recruiting scientists from underrepresented backgrounds to join an immersive in-person mentorship program.
+ Read article ++ OpenMS developers conference 10-16 March 2024, near Malaga, Spain +
+ +We are hosting a developers conference near Malaga, Spain! Click the header above for more information.
+ Read article +New release!
+ Read article ++ Conclusion of the OpenMS Developers Meeting March 27-31, on Kaprije island, Croatia +
+ +The OpenMS Deveopers meeting concluded successfully after several days of fruitful discussions and coding sessions.
+ Read article ++ OpenMS developers meeting March 27-31, on Kaprije island, Croatia +
+ +We are hosting a developers meeting in Croatia soon! Click the header above for more information.
+ Read article +The OpenMS team is proud to present its new website, hosting courtesy of Netlify.
+ Read article ++ New OpenMS read-the-docs manual +
+ +The OpenMS team is proud to present a new OpenMS manual at openms.readthedocs.io
+ Read article +A web-based video help desk for proteomics and metabolomics researchers
+ Read article ++ Second OpenMS documentation update +
+ +The OpenMS team has won a 2022 Google Season of Docs grant to update the OpenMS documentation
+ Read article ++ OpenMS developers meeting April 4-8, 2022 near Corinth, Greece +
+ +We are hosting a developers meeting in Greece soon! Click below for more information.
+ Read article +New release!
+ Read article ++ OpenMS documentation Update Funded by Google Season of Docs +
+ +The OpenMS team has won a 2021 Google Season of Docs grant to update the OpenMS documentation.
+ Read article +New release!
+ Read article ++ Virtual OpenMS Developers Meeting April 15-16, 2021 +
+ +We are hosting a virtual developers meeting soon! Click the header above for more information.
+ Read article +The OpenMS team is proud to present a new OpenMS manual at openms.readthedocs.io. This manual provides much more detail about mass spectrometry including links to relevant sections of University of Tübingen video lectures and a glossary. It also provides more detail about installing OpenMS and it includes the pdf tutorial that was used in classroom presentations of OpenMS. Creation of the manual was supported by grants from Google Season of Docs, from the University of Tübingen and from the Chan-Zuckerberg Initiative Diversity&Inclusion program.
+ +The OpenMS team is proud to present its new website, hosting courtesy of Netlify. The new website uses static HTML and the Hugo theme. Comments, issues or problems with the website (or other OpenMS related matters) can be made thruough the blue button “Help Request” in the top right corner.
+ +OpenMS · News
+We are pleased to announce the 2025 OpenMS Open House.
+Location: Myhal Centre for Engineering Innovation and Entrepreneurship (MY), Room 430, University of Toronto
+Date: November 9th, 2025 From 10am-2pm
+Format: Drop-in session — come by anytime, stay as long or as little as you’d like!
This event offers a great opportunity to:
+The meeting is planned such that one can attend the Open House and HUPO the following week. Note that HUPO requires separate registration.
+
+Click here to register
+
OpenMS was first announced in an abstract for the HUPO fourth Annual World Congress published in Molecular and Cellular Proteomics on 1 August 2005. The OpenMS team invites everyone who has contributed to OpenMS to a BBQ in the garden of Sand at Tübingen University. We estimate that over a hundred individuals have contributed time to OpenMS and we invite all of you to celebrate this milestone. We also acknowledge the support received from CZI, LiBiS, Elixir and de.NBI. For more details ping Tjeerd Dijkstra on discord or by email.
+
+Click here for details and registration
+
+
We are proud to announce the release of OpenMS 2.6.0. Grab it here
+ +We are proud to announce the release of OpenMS 2.7.0. Grab it here
+ +Dear OpenMS-Users,
+we are proud to announce the release of OpenMS 3.0.0. Grab it +here
+In the following you find all important changes to the previous version:
+recent files submenuNew Tools:
+Additionally, the following changes were made to parameters of our TOPP tools:
+| Tool name | +Added/removed | +Parameter name | +Type | +Default value | +Restrictions | +Supported formats | +
|---|---|---|---|---|---|---|
| AssayGeneratorMetabo | ++ | +fingerid:db | +string | ++ | + | + |
| AssayGeneratorMetabo | ++ | +project:loglevel | +string | ++ | + | + |
| AssayGeneratorMetabo | ++ | +project:maxmz | +int | +-1 | ++ | + |
| AssayGeneratorMetabo | ++ | +read_sirius_stdout | +bool | +false | ++ | + |
| AssayGeneratorMetabo | ++ | +sirius:candidates | +int | +10 | +0: | ++ |
| AssayGeneratorMetabo | ++ | +sirius:candidates_per_ion | +int | +1 | ++ | + |
| AssayGeneratorMetabo | ++ | +sirius:db | +string | +none | ++ | + |
| AssayGeneratorMetabo | ++ | +sirius:elements_considered | +string | +SBrClBSe | ++ | + |
| AssayGeneratorMetabo | ++ | +sirius:elements_enforced | +string | +CHNOP | ++ | + |
| AssayGeneratorMetabo | ++ | +sirius:formulas | +string | ++ | + | + |
| AssayGeneratorMetabo | ++ | +sirius:ions_considered | +string | +[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]- | ++ | + |
| AssayGeneratorMetabo | ++ | +sirius:profile | +string | +default | +default,qtof,orbitrap,fticr | ++ |
| AssayGeneratorMetabo | ++ | +sirius:solver | +string | +CLP | ++ | + |
| AssayGeneratorMetabo | ++ | +sirius:tree_timeout | +int | +100 | +0: | ++ |
| AssayGeneratorMetabo | +- | +fingerid:candidates | +int | +10 | +1: | ++ |
| AssayGeneratorMetabo | +- | +fingerid:db | +string | +BIO | ++ | + |
| AssayGeneratorMetabo | +- | +sirius:candidates | +int | +5 | +1: | ++ |
| AssayGeneratorMetabo | +- | +sirius:candidates_per_ion | +int | +-1 | ++ | + |
| AssayGeneratorMetabo | +- | +sirius:db | +string | ++ | + | + |
| AssayGeneratorMetabo | +- | +sirius:elements_considered | +string | ++ | + | + |
| AssayGeneratorMetabo | +- | +sirius:elements_enforced | +string | ++ | + | + |
| AssayGeneratorMetabo | +- | +sirius:formula | +string | ++ | + | + |
| AssayGeneratorMetabo | +- | +sirius:ions_considered | +string | ++ | + | + |
| AssayGeneratorMetabo | +- | +sirius:profile | +string | +qtof | +default,qtof,orbitrap,fticr | ++ |
| AssayGeneratorMetabo | +- | +sirius:tree_timeout | +int | +0 | +0: | ++ |
| CometAdapter | ++ | +PeptideIndexing:allow_nterm_protein_cleavage | +string | +true | +true,false | ++ |
| CometAdapter | ++ | +PeptideIndexing:enzyme:name | +string | +auto | +auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| CometAdapter | ++ | +enzyme | +string | +Trypsin | +Trypsin,Arg-C,Chymotrypsin,CNBr,Asp-N,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage | ++ |
| CometAdapter | ++ | +second_enzyme | +string | ++ | Trypsin,Arg-C,Chymotrypsin,CNBr,Asp-N,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,no cleavage,unspecific cleavage | ++ |
| CometAdapter | +- | +PeptideIndexing:enzyme:name | +string | +auto | +auto,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| CometAdapter | +- | +enzyme | +string | +Trypsin | +Trypsin,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,unspecific cleavage | ++ |
| CometAdapter | +- | +second_enzyme | +string | ++ | Trypsin,Arg-C,Asp-N,Chymotrypsin,CNBr,Lys-C,Lys-N,PepsinA,Trypsin/P,glutamyl endopeptidase,unspecific cleavage | ++ |
| CompNovo | ++ | +algorithm:tryptic_only | +string | +true | +true,false | ++ |
| CompNovo | +- | +algorithm:tryptic_only | +string | +true | ++ | + |
| CompNovoCID | ++ | +algorithm:tryptic_only | +string | +true | +true,false | ++ |
| CompNovoCID | +- | +algorithm:tryptic_only | +string | +true | ++ | + |
| DecoyDatabase | ++ | +enzyme | +string | +Trypsin | +Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| DecoyDatabase | +- | +enzyme | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| Digestor | ++ | +enzyme | +string | +Trypsin | +Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| Digestor | +- | +enzyme | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| DigestorMotif | ++ | +enzyme | +string | +Trypsin | +Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| DigestorMotif | +- | +enzyme | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| FalseDiscoveryRate | ++ | +peptide | +bool | +false | ++ | + |
| FeatureFinderIdentification | ++ | +min_psm_cutoff | +string | +none | ++ | + |
| FeatureFinderIdentification | ++ | +svm:log2_p | +double | ++ | + | + |
| FeatureFinderMetaboIdent | ++ | +candidates_out | +output-file | ++ | + | + |
| FeatureFinderMetaboIdent | +- | +candidates_out | +output-file | ++ | + | *.featureXML | +
| FidoAdapter | ++ | +accuracy | +string | +best | +best,relaxed,sloppy | ++ |
| FidoAdapter | +- | +accuracy | +string | ++ | ,best,relaxed,sloppy | ++ |
| FileConverter | ++ | +include_noise | +bool | +false | ++ | + |
| FileConverter | ++ | +no_zlib_compression | +bool | +false | ++ | + |
| FileFilter | ++ | +f_and_c:remove_hull | +bool | +false | ++ | + |
| GNPSExport | ++ | +out_meta_values | +output-file | ++ | + | *.tsv | +
| GNPSExport | ++ | +out_pairs | +output-file | ++ | + | *.csv | +
| GNPSExport | ++ | +out_quantification | +output-file | ++ | + | *.txt | +
| IDFileConverter | ++ | +fasta_to_mzml:enzyme | +string | +Trypsin | +Chymotrypsin,Trypsin,Arg-C,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| IDFileConverter | +- | +fasta_to_mzml:enzyme | +string | +Trypsin | +Asp-N,Asp-N/B,Asp-N_ambic,Trypsin,Arg-C,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| IDFilter | ++ | +in_silico_digestion:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| IDFilter | ++ | +missed_cleavages:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| IDFilter | +- | +in_silico_digestion:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| IDFilter | +- | +missed_cleavages:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| IDRipper | ++ | +out | +output-prefix | ++ | + | + |
| IDRipper | +- | +out | +output-file | ++ | + | + |
| IsobaricAnalyzer | ++ | +extraction:select_activation | +string | +auto | +auto,Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation,any | ++ |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_126_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_127C_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_127N_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_128C_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_128N_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_129C_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_129N_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_130C_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_130N_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_131C_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_131N_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_132C_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_132N_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_133C_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_133N_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_134C_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_134N_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:channel_135N_description | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:correction_matrix | +string | ++ | + | + |
| IsobaricAnalyzer | ++ | +tmt18plex:reference_channel | +string | +126 | +126,127N,127C,128N,128C,129N,129C,130N,130C,131N,131C,132N,132C,133N,133C,134N,134C,135N | ++ |
| IsobaricAnalyzer | ++ | +type | +string | +itraq4plex | +itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt16plex,tmt18plex,tmt6plex | ++ |
| IsobaricAnalyzer | +- | +extraction:select_activation | +string | +auto | +auto,Collision-induced dissociation,Post-source decay,Plasma desorption,Surface-induced dissociation,Blackbody infrared radiative dissociation,Electron capture dissociation,Infrared multiphoton dissociation,Sustained off-resonance irradiation,High-energy collision-induced dissociation,Low-energy collision-induced dissociation,Photodissociation,Electron transfer dissociation,Pulsed q dissociation,trap-type collision-induced dissociation,beam-type collision-induced dissociation,in-source collision-induced dissociation, | ++ |
| IsobaricAnalyzer | +- | +type | +string | +itraq4plex | +itraq4plex,itraq8plex,tmt10plex,tmt11plex,tmt16plex,tmt6plex | ++ |
| MSFraggerAdapter | ++ | +PeptideIndexing:allow_nterm_protein_cleavage | +string | +true | +true,false | ++ |
| MSFraggerAdapter | ++ | +PeptideIndexing:enzyme:name | +string | +auto | +auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| MSFraggerAdapter | ++ | +digest:search_enzyme_name | +string | +Trypsin | +unspecific cleavage,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage | ++ |
| MSFraggerAdapter | +- | +PeptideIndexing:enzyme:name | +string | +auto | +auto,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin,Arg-C,Arg-C/P,unspecific cleavage | ++ |
| MSFraggerAdapter | +- | +digest:search_enzyme_name | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| MSGFPlusAdapter | ++ | +PeptideIndexing:allow_nterm_protein_cleavage | +string | +true | +true,false | ++ |
| MSGFPlusAdapter | ++ | +PeptideIndexing:enzyme:name | +string | +auto | +auto,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| MSGFPlusAdapter | +- | +PeptideIndexing:enzyme:name | +string | +auto | +auto,Trypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| MSGFPlusAdapter | +- | +add_decoys | +bool | +false | ++ | + |
| MSSimulator | ++ | +algorithm:MSSim:Digestion:enzyme | +string | +Trypsin | +unspecific cleavage,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage | ++ |
| MSSimulator | +- | +algorithm:MSSim:Digestion:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| MapAlignerIdentification | ++ | +model:linear:x_weight | +string | +x | +1/x,1/x2,ln(x),x | ++ |
| MapAlignerIdentification | ++ | +model:linear:y_weight | +string | +y | +1/y,1/y2,ln(y),y | ++ |
| MapAlignerIdentification | +- | +model:linear:x_weight | +string | ++ | 1/x,1/x2,ln(x), | ++ |
| MapAlignerIdentification | +- | +model:linear:y_weight | +string | ++ | 1/y,1/y2,ln(y), | ++ |
| MapAlignerSpectrum | ++ | +model:linear:x_weight | +string | +x | +1/x,1/x2,ln(x),x | ++ |
| MapAlignerSpectrum | ++ | +model:linear:y_weight | +string | +y | +1/y,1/y2,ln(y),y | ++ |
| MapAlignerSpectrum | +- | +model:linear:x_weight | +string | ++ | 1/x,1/x2,ln(x), | ++ |
| MapAlignerSpectrum | +- | +model:linear:y_weight | +string | ++ | 1/y,1/y2,ln(y), | ++ |
| MapAlignerTreeGuided | ++ | +algorithm:model:linear:x_weight | +string | +x | +1/x,1/x2,ln(x),x | ++ |
| MapAlignerTreeGuided | ++ | +algorithm:model:linear:y_weight | +string | +y | +1/y,1/y2,ln(y),y | ++ |
| MapAlignerTreeGuided | +- | +algorithm:model:linear:x_weight | +string | ++ | 1/x,1/x2,ln(x), | ++ |
| MapAlignerTreeGuided | +- | +algorithm:model:linear:y_weight | +string | ++ | 1/y,1/y2,ln(y), | ++ |
| MapRTTransformer | ++ | +model:linear:x_weight | +string | +x | +1/x,1/x2,ln(x),x | ++ |
| MapRTTransformer | ++ | +model:linear:y_weight | +string | +y | +1/y,1/y2,ln(y),y | ++ |
| MapRTTransformer | +- | +model:linear:x_weight | +string | ++ | 1/x,1/x2,ln(x), | ++ |
| MapRTTransformer | +- | +model:linear:y_weight | +string | ++ | 1/y,1/y2,ln(y), | ++ |
| MetaboliteAdductDecharger | ++ | +algorithm:MetaboliteFeatureDeconvolution:negative_mode | +bool | +false | ++ | + |
| MetaboliteAdductDecharger | ++ | +algorithm:MetaboliteFeatureDeconvolution:use_minority_bound | +string | +true | +true,false | ++ |
| MetaboliteAdductDecharger | +- | +algorithm:MetaboliteFeatureDeconvolution:negative_mode | +string | +false | ++ | + |
| MetaboliteAdductDecharger | +- | +algorithm:MetaboliteFeatureDeconvolution:use_minority_bound | +string | +true | ++ | + |
| MetaboliteSpectralMatcher | ++ | +algorithm:merge_spectra | +string | +true | +true,false | ++ |
| MetaboliteSpectralMatcher | ++ | +database | +input-file | ++ | + | .mzML,.msp,*.mgf | +
| MetaboliteSpectralMatcher | ++ | +out_spectra | +output-file | ++ | + | *.mzML | +
| MetaboliteSpectralMatcher | +- | +database | +input-file | ++ | + | *.mzML | +
| MzMLSplitter | ++ | +out | +output-prefix | ++ | + | + |
| MzMLSplitter | +- | +out | +string | ++ | + | + |
| NoiseFilterGaussian | ++ | +algorithm:write_log_messages | +bool | +false | ++ | + |
| NoiseFilterGaussian | +- | +algorithm:write_log_messages | +string | +false | ++ | + |
| NucleicAcidSearchEngine | ++ | +modifications:variable | +string | ++ | io6A,s2U,k2C,m2Gm,Ym,f5Cm,Qbase,ac4Cm,imG-14,cm5s2U,mnm5s2U,m227G,yW-58,I,g6A,nm5U,m7G,s2Um,Y,hm5C,m5U,preQ0,o2yW,m5Um,preQ1,m66Am,ac6A,ms2io6A,Am,Im,mnm5U,m22G,t6A,m8A,m7GpppN,m27GpppN,m227GpppN,mpppN,m28A,acp3D,acp3Y,imG,D,N,C+,m27Gm,ho5C,inm5U,inm5Um,inm5s2U,pppN,GpppN,CoApN,m44C,acCoApN,malonyl-CoApN,succinyl-CoApN,ppN,NADpN,m6t6A,OHyWy,pG(pN),ncm5s2U,nchm5U,mchm5Um,pN,ges2U,cmnm5ges2U,mnm5ges2U,nm5ges2U,m5D,mmpN,mpN,5'-OH-N,N2'3'cp,ct6A,hm6A,f6A,cnm5U,mcmo5Um,m5C,ms2ct6A,ht6A,msms2i6A,hm5Cm,pY,pm5C,ps2U,hn6A,pD,pm2G,pm66A,pGm,pm5U,pm22G,pm3U,m5Cm,Ar(p),pac4C,pCm,pppG,pm7G,pm1A,pUm,pAm,pm4Cm,pC2'3'cp,tm5U,pm6A,pyW,pm1G,pA2'3'cp,ps4U,pI,ppG,pm2A,m1G,pmcm5s2U,cmnm5Um,pse2U,pt6A,pf5C,pppA,pG,pG2'3'cp,pms2i6A,pcmo5U,pyW,Xm,pm44C,pi6A,phm5C,pU,pAr(p),pac4Cm,pGp,m1I,pU2'3'cp,mcm5U,Gm,pm4C,ncm5Um,pm5Um,pmnm5U,pm3C,m5s2U,yW,pC,pm6t6A,f5C,pAp,m1Am,m1Im,ApppN,AppppN,ApppppN,m6ApppN,m6AppppN,m6ApppppN,m7GppppN,Gr(p),pm1Am,pm1Gm,pm1Im,pm1acp3Y,pm1I,pm1Y,pk2C,ps2C,pm1acp3Y,pm3Y,nm5s2U,pm5Cm,pmchm5U,pinm5Um,pinm5s2U,pinm5U,pnm5U,pncm5U,pchm5U,pcmnm5U,pcm5U,m2G,pho5U,pmcm5Um,pmcm5U,pmo5U,pm5D,pmimG,phm5Cm,pIm,pYm,pmcmo5Um,m2A,pGr(p),pm28A,pmsms2i6A,pges2U,pms2ct6A,pms2io6A,pms2hn6A,pms2m6A,pms2t6A,ps2Um,pm3Um,pacp3D,pacp3U,pimG-14,pmchm5Um,pnm5ges2U,pnm5se2U,pnm5s2U,pnchm5U,pncm5Um,m4Cm,pncm5s2U,pcm5s2U,pcmnm5Um,pcmnm5ges2U,pcmnm5se2U,pcmnm5s2U,pcnm5U,pf5Cm,pho5C,pm5s2U,m27G,m22Gm,pmnm5ges2U,pmnm5se2U,pmnm5s2U,ptm5s2U,ptm5U,pyW-86,pyW-72,pyW-58,ppreQ1,ppreQ0,m66A,pm8A,pC+,pG+,pct6A,poQ,pgalQ,pgluQ,pht6A,pOHyW,pimG2,gluQ,pmanQ,pOHyWy,pm27Gm,pQ,pOHyWx,pmcmo5U,pimG,pm44Cm,pm2Gm,pm22Gm,ncm5U,pm6Am,pm66Am,pio6A,pac6A,pf6A,pg6A,phm6A,phn6A,cm5U,pm27G,pm227G,pm27Gm,pA,cmnm5s2U,cmo5U,m3Y,m3U,ms2m6A,Um,ms2i6A,m3C,cmnm5se2U,ms2t6A,i6A,m3Um,mcmo5U,mimG,oQ,preQ1base,nm5se2U,m1Gm,ho5U,Q,xG,mcm5s2U,m44Cm,s4U,xC,yW-86,xA,chm5U,mo5U,acp3U,xU,yW-72,mnm5se2U,ms2hn6A,m1acp3Y,mcm5Um,ac4C,m6Am,m1A,Cm,mchm5U,galQ,cmnm5U,m1Y,imG2,m4C,manQ,tm5s2U,s2C,OHyWx,se2U,preQ0base,m6A,OHyW,xX,G+,3'-p,5'-p,5'-p*,3'-c,mA,mC,mG,mU,sU,mmA,mAm,mCm,mGm,mUm,cmo5U/chm5U,mchm5U/mcmo5U,mchm5Um/mcmo5Um,m6t6A/hn6A,galQ/manQ,mA?,mC?,mG?,mU?,mI?,msU?,mmA?,mmC?,mmG?,mmmG?,ac4C/f5Cm?,acp3U/cmnm5Um?,dA,dC,dG,dU,dT,A*,C*,G*,U*,dA*,dC*,dG*,dU*,dT* | ++ |
| NucleicAcidSearchEngine | +- | +modifications:variable | +string | ++ | m1Am,m1Gm,m1Im,m1acp3Y,m1A,m1G,m1I,m1Y,m28A,msms2i6A,ges2U,k2C,m2A,ms2ct6A,ms2io6A,ms2hn6A,ms2i6A,ms2m6A,ms2t6A,se2U,s2Um,s2C,s2U,Am,Cm,Gm,Im,Ym,Um,mcmo5Um,Ar(p),Gr(p),(pN)2'3'>p,hm5Cm,m3Um,acp3D,acp3Y,acp3U,m3C,m3Y,m3U,imG-14,s4U,m5Cm,m5Um,mchm5Um,mchm5U,inm5s2U,inm5Um,inm5U,nm5ges2U,nm5se2U,nm5s2U,nm5U,nchm5U,ncm5s2U,ncm5Um,ncm5U,chm5U,cm5s2U,cmnm5ges2U,cmnm5se2U,cmnm5s2U,cmnm5Um,cmnm5U,cm5U,cnm5U,f5Cm,f5C,ho5C,hm5C,ho5U,mcm5s2U,mcm5Um,mcm5U,mo5U,m5s2U,mnm5ges2U,mnm5se2U,mnm5s2U,mnm5U,m5C,m5D,m5U,tm5s2U,tm5U,CoA(pN),acCoA(pN),malonyl-CoA(pN),succinyl-CoA(pN),p(pN),5'-OH-N,(pN),NAD(pN),pp(pN),yW-86,yW-72,yW-58,preQ1tRNA,preQ0tRNA,m7G,m7Gpp(pN),m8A,m2Gm,m27Gm,m27G,m27Gpp(pN),m22Gm,m227G,m227Gpp(pN),m22G,m2G,m4Cm,m44Cm,m44C,ac4Cm,ac4C,m4C,m6Am,m66Am,m66A,io6A,ac6A,f6A,g6A,hm6A,hn6A,i6A,m6t6A,m6A,t6A,Qbase,C+,mm(pN),m(pN),G+,ct6A,D,oQ,galQ,mpp(pN),gluQ,pG(pN),Gpp(pN),ht6A,OHyW,I,imG2,manQ,OHyWy,mimG,o2yW,preQ0base,preQ1base,Y,Q,OHyWx,Xm,xX,xA,xC,xG,xU,N,cmo5U,mcmo5U,yW,imG,dA,dC,dG,dU,dT,3'-p,5'-p,mA,mC,mG,mU,sU,mmA,mAm,mCm,mGm,mUm,cmo5U/chm5U,mchm5U/mcmo5U,mchm5Um/mcmo5Um,m6t6A/hn6A,galQ/manQ,mA?,mC?,mG?,mU?,mI?,msU?,mmA?,mmC?,mmG?,mmmG?,ac4C/f5Cm?,acp3U/cmnm5Um? | ++ |
| OpenPepXL | ++ | +peptide:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| OpenPepXL | +- | +peptide:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| OpenPepXLLF | ++ | +peptide:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| OpenPepXLLF | +- | +peptide:enzyme | +string | +Trypsin | +Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Trypsin,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| OpenSwathAnalyzer | ++ | +algorithm:strict | +string | +true | +true,false | ++ |
| OpenSwathAnalyzer | +- | +algorithm:strict | +string | +true | ++ | + |
| OpenSwathFileSplitter | ++ | +outputDirectory | +output-prefix | +./ | ++ | + |
| OpenSwathFileSplitter | +- | +outputDirectory | +string | +./ | ++ | + |
| OpenSwathRTNormalizer | ++ | +algorithm:strict | +string | +true | +true,false | ++ |
| OpenSwathRTNormalizer | +- | +algorithm:strict | +string | +true | ++ | + |
| OpenSwathWorkflow | ++ | +Scoring:strict | +string | +true | +true,false | ++ |
| OpenSwathWorkflow | ++ | +pasef | +bool | +false | ++ | + |
| OpenSwathWorkflow | +- | +Scoring:strict | +string | +true | ++ | + |
| PeptideIndexer | ++ | +allow_nterm_protein_cleavage | +string | +true | +true,false | ++ |
| PeptideIndexer | ++ | +enzyme:name | +string | +auto | +auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| PeptideIndexer | +- | +enzyme:name | +string | +auto | +auto,Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| PrecursorIonSelector | ++ | +algorithm:Preprocessing:store_peptide_sequences | +bool | +false | ++ | + |
| PrecursorIonSelector | +- | +algorithm:Preprocessing:store_peptide_sequences | +string | +false | ++ | + |
| ProteinQuantifier | ++ | +method | +string | +top | +top,iBAQ | ++ |
| ProteinQuantifier | ++ | +top:N | +int | +3 | +0: | ++ |
| ProteinQuantifier | ++ | +top:aggregate | +string | +median | +median,mean,weighted_mean,sum | ++ |
| ProteinQuantifier | ++ | +top:include_all | +bool | +false | ++ | + |
| ProteinQuantifier | +- | +average | +string | +median | +median,mean,weighted_mean,sum | ++ |
| ProteinQuantifier | +- | +include_all | +bool | +false | ++ | + |
| ProteinQuantifier | +- | +top | +int | +3 | +0: | ++ |
| ProteomicsLFQ | ++ | +Alignment:model:linear:x_weight | +string | +x | +1/x,1/x2,ln(x),x | ++ |
| ProteomicsLFQ | ++ | +Alignment:model:linear:y_weight | +string | +y | +1/y,1/y2,ln(y),y | ++ |
| ProteomicsLFQ | ++ | +FDR_type | +string | +PSM | +PSM,PSM+peptide | ++ |
| ProteomicsLFQ | ++ | +PeptideQuantification:min_psm_cutoff | +string | +none | ++ | + |
| ProteomicsLFQ | ++ | +PeptideQuantification:svm:log2_p | +double | ++ | + | + |
| ProteomicsLFQ | ++ | +ProteinQuantification:method | +string | +top | +top,iBAQ | ++ |
| ProteomicsLFQ | ++ | +ProteinQuantification:top:N | +int | +3 | +0: | ++ |
| ProteomicsLFQ | ++ | +ProteinQuantification:top:aggregate | +string | +median | +median,mean,weighted_mean,sum | ++ |
| ProteomicsLFQ | ++ | +ProteinQuantification:top:include_all | +string | +true | +true,false | ++ |
| ProteomicsLFQ | ++ | +picked_proteinFDR | +bool | +false | ++ | + |
| ProteomicsLFQ | +- | +Alignment:model:linear:x_weight | +string | ++ | 1/x,1/x2,ln(x), | ++ |
| ProteomicsLFQ | +- | +Alignment:model:linear:y_weight | +string | ++ | 1/y,1/y2,ln(y), | ++ |
| ProteomicsLFQ | +- | +ProteinQuantification:average | +string | +median | +median,mean,weighted_mean,sum | ++ |
| ProteomicsLFQ | +- | +ProteinQuantification:include_all | +string | +true | +true,false | ++ |
| ProteomicsLFQ | +- | +ProteinQuantification:top | +int | +3 | +0: | ++ |
| ProteomicsLFQ | +- | +picked_proteinFDR | +string | +false | ++ | + |
| QualityControl | ++ | +in_fasta | +input-file | ++ | + | *.fasta | +
| QualityControl | ++ | +out_msms | +string | ++ | + | + |
| RNPxlSearch | ++ | +peptide:enzyme | +string | +Trypsin | +Arg-C,Trypsin,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| RNPxlSearch | +- | +peptide:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| SimpleSearchEngine | ++ | +Search:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Asp-N/B,CNBr,Formic_acid,Asp-N,Chymotrypsin/P,Chymotrypsin,Asp-N_ambic,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| SimpleSearchEngine | +- | +Search:enzyme | +string | +Trypsin | +Trypsin,Arg-C,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| SiriusAdapter | ++ | +fingerid:db | +string | ++ | + | + |
| SiriusAdapter | ++ | +out_annotated_spectra | +output-file | ++ | + | *.mzML | +
| SiriusAdapter | ++ | +project:loglevel | +string | ++ | + | + |
| SiriusAdapter | ++ | +project:maxmz | +int | +-1 | ++ | + |
| SiriusAdapter | ++ | +read_sirius_stdout | +bool | +false | ++ | + |
| SiriusAdapter | ++ | +sirius:candidates | +int | +10 | +0: | ++ |
| SiriusAdapter | ++ | +sirius:candidates_per_ion | +int | +1 | ++ | + |
| SiriusAdapter | ++ | +sirius:db | +string | +none | ++ | + |
| SiriusAdapter | ++ | +sirius:elements_considered | +string | +SBrClBSe | ++ | + |
| SiriusAdapter | ++ | +sirius:elements_enforced | +string | +CHNOP | ++ | + |
| SiriusAdapter | ++ | +sirius:formulas | +string | ++ | + | + |
| SiriusAdapter | ++ | +sirius:ions_considered | +string | +[M+H]+,[M+K]+,[M+Na]+,[M+H-H2O]+,[M+H-H4O2]+,[M+NH4]+,[M-H]-,[M+Cl]-,[M-H2O-H]-,[M+Br]- | ++ | + |
| SiriusAdapter | ++ | +sirius:profile | +string | +default | +default,qtof,orbitrap,fticr | ++ |
| SiriusAdapter | ++ | +sirius:solver | +string | +CLP | ++ | + |
| SiriusAdapter | ++ | +sirius:tree_timeout | +int | +100 | +0: | ++ |
| SiriusAdapter | ++ | +sirius_user_email | +string | ++ | + | + |
| SiriusAdapter | ++ | +sirius_user_password | +string | ++ | + | + |
| SiriusAdapter | +- | +fingerid:candidates | +int | +10 | +1: | ++ |
| SiriusAdapter | +- | +fingerid:db | +string | +BIO | ++ | + |
| SiriusAdapter | +- | +project:processors | +int | +1 | ++ | + |
| SiriusAdapter | +- | +sirius:candidates | +int | +5 | +1: | ++ |
| SiriusAdapter | +- | +sirius:candidates_per_ion | +int | +-1 | ++ | + |
| SiriusAdapter | +- | +sirius:db | +string | ++ | + | + |
| SiriusAdapter | +- | +sirius:elements_considered | +string | ++ | + | + |
| SiriusAdapter | +- | +sirius:elements_enforced | +string | ++ | + | + |
| SiriusAdapter | +- | +sirius:formula | +string | ++ | + | + |
| SiriusAdapter | +- | +sirius:ions_considered | +string | ++ | + | + |
| SiriusAdapter | +- | +sirius:profile | +string | +qtof | +default,qtof,orbitrap,fticr | ++ |
| SiriusAdapter | +- | +sirius:tree_timeout | +int | +0 | +0: | ++ |
| SpectraMerger | ++ | +algorithm:average_gaussian:ms_level | +int | +1 | +0: | ++ |
| SpectraMerger | ++ | +algorithm:average_gaussian:precursor_mass_tol | +double | +0.0 | +0.0: | ++ |
| SpectraMerger | ++ | +algorithm:average_gaussian:precursor_max_charge | +int | +1 | +1: | ++ |
| SpectraMerger | ++ | +algorithm:average_tophat:ms_level | +int | +1 | +0: | ++ |
| SpectraMerger | ++ | +algorithm:precursor_method:mass_tolerance | +double | +0.0 | +0.0: | ++ |
| SpectraMerger | +- | +algorithm:average_gaussian:ms_level | +int | +1 | +1: | ++ |
| SpectraMerger | +- | +algorithm:average_tophat:ms_level | +int | +1 | +1: | ++ |
| TextExporter | ++ | +consensus:add_metavalues | +bool | +false | ++ | + |
| XTandemAdapter | ++ | +PeptideIndexing:allow_nterm_protein_cleavage | +string | +true | +true,false | ++ |
| XTandemAdapter | ++ | +PeptideIndexing:enzyme:name | +string | +auto | +auto,Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage | ++ |
| XTandemAdapter | ++ | +enzyme | +string | +Trypsin | +Trypsin,Arg-C,Chymotrypsin,Asp-N_ambic,Chymotrypsin/P,CNBr,Asp-N/B,Formic_acid,Asp-N,Arg-C/P,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,no cleavage,unspecific cleavage | ++ |
| XTandemAdapter | +- | +PeptideIndexing:enzyme:name | +string | +auto | +auto,leukocyte elastase,proline endopeptidase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,iodosobenzoate,staphylococcal protease/D,proline-endopeptidase/HKR,Glu-C+P,PepsinA + P,cyanogen-bromide,Clostripain/P,Arg-C/P,Asp-N,Asp-N/B,Asp-N_ambic,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,elastase-trypsin-chymotrypsin,no cleavage,unspecific cleavage,Arg-C,Trypsin | ++ |
| XTandemAdapter | +- | +enzyme | +string | +Trypsin | +Asp-N,Asp-N/B,Asp-N_ambic,unspecific cleavage,Arg-C/P,Chymotrypsin,Chymotrypsin/P,CNBr,Formic_acid,Lys-C,Lys-N,Lys-C/P,PepsinA,TrypChymo,Trypsin/P,V8-DE,V8-E,leukocyte elastase,glutamyl endopeptidase,Alpha-lytic protease,2-iodobenzoate,Trypsin,Arg-C | ++ |
Best regards, +The OpenMS-Developers
+ +Dear OpenMS-Users,
+we are proud to announce the release of OpenMS 3.2. Grab it here
+In the following you find all important changes to the previous version:
+What’s new:
+Library:
+New Tools:
+Fixes:
+Misc:
+Changed/new parameters: see CHANGELOG_PARAMS for details
+Note: The goal of our library is to provide useful, reusable code in a way that’s easy to understand and use. +To make OpenMS simpler, more focused and more accessible we gradually remove potentially outdated tools and algorithms. +If you, as a user, are negatively affected by this step please contact us. We listen to our users and will try to find +an alternative solution or reverse a particular decision for removal.
+Cleanup/Removal:
+removed tools:
+removed library code:
+removed tutorials:
+removed tests:
+Deprecated (and likely removed in the next release)
+Best regards, +The OpenMS-Developers
+ +Dear OpenMS-Users,
+we are proud to announce the release of OpenMS 3.3. Grab it here
+Important changes to the previous version:
+What’s new:
+Misc:
+Fixes:
+Best regards, +The OpenMS-Developers
+ +Dear OpenMS-Users,
+We are proud to announce the release of OpenMS 3.4.1. Grab it here
+In the following you find all important changes to the previous version:
+Documentation:
+Fixes:
+General:
+Dependencies:
+OpenSwath:
+im_range to scoreIdentification_ instead of computing it in the function. Addresses issue #7883. (PR #7885)Misc:
+Fixes:
+Library:
+Removed tools:
+Best regards, +The OpenMS-Developers
+ +Dear OpenMS-Users,
+We are proud to announce the release of OpenMS 3.5. Grab it here.
+A couple of things are different this time:
+In the following you find all important changes to the previous version:
+NOTICE: 3.5.0 is going to be the last official release for MacOS on Intel processors. If you need support for OpenMS on that platform moving forward, please contact us.
+Speed improvements:
+Linux arm64 support:
+MSSpectrum.get_df(), MSChromatogram.get_df(), ConsensusMap.get_metadata_df(), FeatureMap.get_df(). Example changes: RT → rt, MZ → mz, nativeID → native_id, precursorMZ → precursor_mz. Update code that references old column names.__len__() for MSSpectrum, MSChromatogram, MSExperiment, AASequence (#8151, #8415, #8417)__str__() and __repr__() for core classes (#8429)get_df() method (#8435)FileFilter:
+SageAdapter:
+CometAdapter:
+DecoyDatabase:
+MassTraceExtractor:
+FeatureFinderCentroided, FeatureFinderMetabo, FeatureFinderMultiplex:
+FeatureFinderMetaboIdent, FeatureFinderIdentification:
+--combineIonMobilitySpectra option). IM values can be specified in the input TSV/idXML.NucleicAcidSearchEngine:
+Digestor:
+All:
+IonMobilityBinning:
+FLASHDeconv:
+setIMFormat()/getIMFormat() API for per-spectrum ion mobility format tracking. (#8177)setTargetDecoyType()/getTargetDecoyType(); supports target+decoy peptide hits.findScoreType() method for generic score type detection. Checks if main score matches requested ScoreType (PEP, QVAL, FDR, etc.) or finds it in meta values.setTargetDecoyType()/getTargetDecoyType().isDecoy().assignRanks and sortByRanks in PeptideIdentifications and sort and filter by score instead. Also removed updateHitRanks in IDFilter (#7991)std::vector<PeptideIdentification> now is encapsulated in a class PeptideIdentificationList.EnzymaticDigestion.semiSpecificDigestion_()Best regards,
+The OpenMS-Developers
OpenMS · News
+The OpenMS team is excited to announce that the 2026 Rising Star in +Computational Mass Spectrometry recipient is Maria Llambrich +Rodriguez. +Maria’s innovative contributions to computational mass spectrometry and +commitment to open-source code represent the impact this award aims to +highlight. Congratulations, Maria!
+The Rising Star in Computational Mass Spectrometry is an initiative +launched in collaboration with our partner society, Females in Mass +Spectrometry, to recognize and spotlight +early-career scientists in the field. We are grateful to everyone +involved in helping make this annual award a tradition.
+Thank you to our sponsor, The Chan Zuckerberg +Initiative.
+ +OpenMS · News
+The OpenMS team and Steffen Neumann from CIBI will teach four workshops in South Africa.
+
+Topic: Plant Proteomics and Metabolomics
+
+The workshop highlights the technologies of metabolomics and proteomics for plant biotechnology. Equal time will be given to lectures and hands-on exercises. Topics include an introduction to biological liquid chromatography tandem mass spectrometry (LC-MS/MS), targeted and untargeted methods for metabolomics, metabolite identification, quantitation in LC-MS/MS, web resources for plant molecular biology, ontologies for plant research, and RNA-Seq for organisms lacking published genomes.
+
We are pleased to announce the 2024 OpenMS User Meeting.
+When: 17 and 18 October 2024.
+Where: KNIME GmbH, Körtestr. 10, 10967 Berlin, Germany.
+What:
The meeting is planned such that one can attend the OpenMS user meeting in Berlin 17-18 October and HUPO in Dresden 20-24 October 2024. Note that HUPO requires separate registration.
+
+Click here to register
+
+ 
+
+
OpenMS-lib
++ OpenMS-lib is a mature and reliable C++ framework for omics based mass spectrometry data analysis. +
+ +Overview
+20+ years of development
+Open source under the BSD-3 clause license
+Backed by an active community of researchers and developers
+High performance and optimized for scale
+Pipeline
+Modular command-line tools covering the complete MS analysis pipeline
++ Chain them together to build custom workflows tailored to your data. +
++ Integrates with common workflow engines + Learn More +
+Get started
+For Developers
+Your improvements help researchers worldwide.
+How to propose changes, open pull requests, and work with the OpenMS community.
+ + Read guidelines + +File bugs, request features, or discuss changes on the OpenMS tracker.
+ + Report an issue + +Platform-specific guides for compiling OpenMS-lib locally.
+ +Architecture, coding standards, and contribution workflows for OpenMS-lib.
+ + Read the manual + +Step-by-step guide for adding a new tool to the TOPP pipeline suite.
+ + Add a TOPP tool + +Answers to common questions about building, testing, and contributing.
+ + Read the FAQ + +On this pageWe would like to make it easy for you to include the OpenMS project identity in your next academic paper, course materials, or presentation.
+You will find several high-resolution versions of the OpenMS logo here. Note that by using the openms.org resources, you accept the OpenMS Code of Conduct.
+ +On this pageOur website address is: http(s)://www.openms.de
+When visitors leave comments on the site we collect the data shown in the comments form, and also the visitor’s IP address and browser user agent string to help spam detection.
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+Visitor comments may be checked through an automated spam detection service.
+ +Research
+A curated bibliography of scientific publications that reference OpenMS software, methods, and workflows. Showing publications from the two most recent years. Use the dropdown to switch between them.
+ +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
pyopenms_viz
++ Create spectra, chromatograms and more from just a single line of code. +
+ + + +Contribute
+Python
++ Python bindings to OpenMS-lib. Write custom analysis scripts and integrate OpenMS + into Python workflows. +
+Run OpenMS-lib algorithms directly in Python
+Pandas DataFrame export for common OpenMS-lib datastructures
+Run in scripts or in Jupyter Notebooks
+Seamless integration with the scientific Python stack
+Run pyOpenMS in your browser without a local install.
+ +Developers
+Any class in OpenMS-lib can be easily wrapped and used with PyOpenMS.
+On this pageThis is the manual followed by openms’s Code of Conduct Committee. It’s used when we respond to an issue to make sure we’re consistent and fair.
+Enforcing the Code of Conduct impacts our community today and for the future. It’s an action that we do not take lightly. When reviewing enforcement measures, the Code of Conduct Committee will keep the following values and guidelines in mind:
+Voluntary informal mediation is a tool at our disposal. In contexts such as when two or more parties have all escalated to the point of inappropriate behavior (something sadly common in human conflict), it may be useful to facilitate a mediation process. This is only an example: the Committee can consider mediation in any case, mindful that the process is meant to be strictly voluntary and no party can be pressured to participate. If the Committee suggests mediation, it should:
+The mediator will engage with all the parties and seek a resolution that is satisfactory to all. Upon completion, the mediator will provide a report (vetted by all parties to the process) to the Committee, with recommendations on further steps. The Committee will then evaluate these results (whether a satisfactory resolution was achieved or not) and decide on any additional action deemed necessary.
+When the Committee (or a Committee member) receives a report, they will first determine whether the report is about a clear and severe breach (as defined below). If so, immediate action needs to be taken in addition to the regular report handling process.
+We know that it is painfully common for internet communication to start at or devolve into obvious and flagrant abuse. We will deal quickly with clear and severe breaches like personal threats, violent, sexist or racist language.
+When a member of the Code of Conduct Committee becomes aware of a clear and severe breach, they will do the following:
+When a report is sent to the Committee they will immediately reply to the reporter to confirm receipt. This reply must be sent within 72 hours, and the group should strive to respond much quicker than that.
+If a report doesn’t contain enough information, the Committee will obtain all relevant data before acting. The Committee is empowered to act on the Executive Committee’s behalf in contacting any individuals involved to get a more complete account of events.
+The Committee will then review the incident and determine, to the best of their ability:
+This information will be collected in writing, and whenever possible the group’s deliberations will be recorded and retained (i.e. chat transcripts, email discussions, recorded conference calls, summaries of voice conversations, etc).
+It is important to retain an archive of all activities of this Committee to ensure consistency in behavior and provide institutional memory for the project. To assist in this, the default channel of discussion for this Committee will be a private mailing list accessible to current and future members of the Committee as well as members of the Executive Committee upon justified request. If the Committee finds the need to use off-list communications (e.g. phone calls for early/rapid response), it should in all cases summarize these back to the list so there’s a good record of the process.
+The Code of Conduct Committee should aim to have a resolution agreed upon within two weeks. In the event that a resolution can’t be determined in that time, the Committee will respond to the reporter(s) with an update and projected timeline for resolution.
+The Committee must agree on a resolution by consensus. If the group cannot reach consensus and deadlocks for over a week, the group will turn the matter over to the Executive Committee for resolution.
+Possible responses may include:
+Once a resolution is agreed upon, but before it is enacted, the Committee will contact the original reporter and any other affected parties and explain the proposed resolution. The Committee will ask if this resolution is acceptable, and must note feedback for the record.
+Finally, the Committee will make a report to the OpenMS Executive Committee (as well as the OpenMS core team in the event of an ongoing resolution, such as a ban).
+The Committee will never publicly discuss the issue; all public statements will be made by the chair of the Code of Conduct Committee or the OpenMS Executive Committee.
+In the event of any conflict of interest, a Committee member must immediately notify the other members, and recuse themselves if necessary.
+ +Partner with OpenMS
+OpenMS grows through long-term collaboration with universities, institutes, and research groups that contribute software, methods, and training as part of their work.
+ +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. +
+
+
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+
+
+
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+
+
+
+
+
+ + 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. +
+Support OpenMS
+Sponsorship provides direct funding for software engineering, documentation, community events, and the long-term sustainability of the OpenMS ecosystem.
+ +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. +
+Foundation sponsorship is how organizations contribute substantially to OpenMS Inc. In return, sponsors receive public acknowledgment on this site and other channels appropriate to their level—similar to tiered programs used by foundations such as the Apache Software Foundation.
+ +$250,000 annually
+Shaping the future of Open Science
+For organizations committed to shaping the future of open scientific infrastructure.
+$50,000 annually
+Strategic investor in Open Science
+Strategic investment in open scientific infrastructure.
+$10,000 annually
+Strong Supporter of Open Science
+Strong support for OpenMS training, outreach, and community programs.
+Impact: Directly support training programs, workshops, and research initiatives.
+$5,000 annually
+Supporter of Open Science
+Public recognition for organizations supporting the OpenMS ecosystem.
+Contribution levels are agreed individually. To get started, contact us via the form below. OpenMS Inc. is a U.S. 501(c)(3) public charity; U.S.-based sponsors may be eligible for tax benefits where permitted by law.
++ OpenMS receives direct funding from the organizations below. We are grateful for + their support of open-source mass spectrometry software. +
+
+
+
+ + 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. +
+On this pageLast updated January 4, 2020
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+ +Run locally or deploy with docker-compose
+Python-based pipeline creation and frontend development
+Auto-generates UI for TOPP tools
+Customizable visualizations and results display
+Workspaces for user data with unique shareable IDs
+Fork and customize the template for your pipeline.
+ + Fork Template + +Host multiple WebApps together with Docker Compose.
+ + Deploy with docker compose + +Package your WebApp as a standalone Windows executable.
+Community apps built on the OpenMS WebApps framework.
+GUI or Command Line Apps actively maintained by the OpenMS core development team
+
+ Web-based analysis and visualization of top-down proteomics data
++ Maintainers + Tom Muller, Kyowon Jeong +
+ +
+ Interactive DIA proteomics data analysis
++ Maintainers + Justin Sing +
+ +
+ Web-based access to the umetaflow pipeline
+ +
+ Web-based workflow for DDA proteomics
++ Maintainers + Tom Müller +
+ +
+ Web-based access to the nucleic acid search engine (NASE)
++ Maintainers + Sam Wein +
+ +
+ Web-based analysis pipeline for XL-MS data
++ Maintainers + Arslan Siraj +
+ +
+ Web-based analysis pipeline for immunopeptidomics
++ Maintainers + Jonas Scheid +
+ ++ Don't see your functionality tool? Contact us. +
+These projects are not directly maintained by the OpenMS team but are dependent on OpenMS infrastructure or funding.
+Next generation file format for mass spectrometry run files, built on top of Apache Parquet
++ Maintainers + Joshua Klein, Sam Wein, Tim Van Den Bossche, Peter Jones, Oliver Kohlbacher +
+ +An open-source ecosystem for large-scale quantitative proteomics.
++ Maintainers + Yasset Perez-Riverol, Mingze Bai, Timo Sachsenberg, Chengxin Dai, Julianus Pfeuffer +
+ +De Novo Mass Spectrometry Peptide Sequencing with a Transformer Model
++ Maintainers + Wout Bittremieux, Bill Noble +
+ +Spectral library generation tool for DIA.
++ Maintainers + Justin Sing +
+ +Semi-supervised learning and scoring of OpenSWATH results
++ Maintainers + Justin Sing +
+ ++ Don't see your functionality tool? Contact us. +
+These apps are no longer actively maintained. They remain available as-is and may still be useful for your analysis, but we recommend checking for known limitations or compatibility issues before use. If you're interested in maintaining or reviving one, we'd love to hear from you.
+A bioinformatics analysis pipeline used for quantitative processing of data independent (DIA) proteomics data.
+ +Interested in reviving one of these projects?
+Contribute
+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
++ 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). +
+@article{sachsenberg2014metaprosip,
-title={MetaProSIP: automated inference of stable isotope incorporation
- rates in proteins for functional metaproteomics},
-author={Sachsenberg, Timo and Herbst, Florian-Alexander and Taubert, Martin and Kermer, Ren{\'e}
- and Jehmlich, Nico and von Bergen, Martin and Seifert, Jana and Kohlbacher, Oliver},
-journal={Journal of proteome research},
-year={2014},
-publisher={ACS Publications}
-}
-