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This repository was archived by the owner on Apr 9, 2026. It is now read-only.
By following these steps, you’re instructing macOS to trust the OpenMS installer and allow its execution. Ensure that you’ve downloaded the installer from a **trusted source** (i.e., build archive of the Unversity of Tübingen or OpenMS' GitHub artifacts) before proceeding.
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By following these steps, you’re instructing macOS to trust the OpenMS installer and allow its execution. Ensure that you’ve downloaded the installer from a **trusted source** (i.e., build archive of the Unversity of Tübingen or OpenMS' GitHub artifacts) before proceeding.
To use {term}`TOPP` as regular app in the shell, add the following lines to the `~/.profile` file.
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:::{warning} Known Installer Issues
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1. Nothing happens when you click OpenMS apps or the validity of the developer could not be confirmed.
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This usually means the OpenMS software lands in quarantine even after installation of the `.pkg`. This was more common with our older `.dmg` image but may still happen.
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Since macOS Catalina (maybe also Mojave) all apps and executables have to be officially notarized by Apple but we
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currently do not have the resources for a streamlined notarization workflow.
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cd /Applications/OpenMS-<version>
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sudo xattr -r -d com.apple.quarantine *
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```
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2. Bug with running Java based thirdparty tools like {term}`MSGFPlusAdapter` and {term}`LuciphorAdapter` from within **TOPPAS.app**
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If you face issues while running Java based thirdparty tools from within {term}`TOPPAS.app <TOPPAS>`, run the {term}`TOPPAS.app <TOPPAS>`
Copy file name to clipboardExpand all lines: docs/about/installation/installation-on-windows.md
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To Install the binary package of OpenMS & {term}`TOPP`:
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1. Download the installer `OpenMS-<version>-Win64.exe` from the [archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/)
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1. Download the installer `OpenMS-<version>-Win64.exe` from the [archive](https://abibuilder.cs.uni-tuebingen.de/archive/openms/OpenMSInstaller/release/latest/)
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2. Execute the installer under the user account that later runs OpenMS and follow its instructions.
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You may see a Windows Defender Warning, since our installer is not digitally signed.
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Click on "More Info", and then "Run anyways".
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When asked for an admin authentication, please enter the credentials (it is not advised to directly invoke the installer using an admin account).
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4. For Win8 or later, Windows will report an error while installing `.net4` as it's mostly included. But it might occur
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that `.net3.5` does not get properly installed during the process.
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Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://docs.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows).aspx#ControlPanel) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third party tools (ProteoWizard).
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Fix is to enable the .NET Framework 3.5 yourself through Control Panel. See this [Microsoft help page](https://docs.microsoft.com/en-us/dotnet/framework/install/dotnet-35-windows#enable-the-net-framework-35-in-control-panel) for detailed information. Even if this step fails, this does not affect the functionality of OpenMS, except for the executability of included third party tools (ProteoWizard).
Copy file name to clipboardExpand all lines: docs/about/learning/background.md
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Learning
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========
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Proteomics and metabolomics focus on complex interactions within biological systems; the former is centered on proteins while the latter is based on metabolites. To understand these interactions, we need to accurately identify the different biological components involved.
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Proteomics and metabolomics focus on complex interactions within biological systems; the former is centered on proteins while the latter is based on metabolites. To understand these interactions, we need to accurately identify the different biological components involved.
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{term}`Liquid chromatography` (LC) and {term}`mass spectrometry` (MS) are the analytical techniques used to isolate and identify biological components in proteomics and metabolomics. LC-MS data can be difficult to analyze manually given its amount and complexity. Therefore, we need specialized software that can analyze high-throughput LC-MS data quickly and accurately.
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{term}`Liquid chromatography` (LC) and {term}`mass spectrometry` (MS) are the analytical techniques used to isolate and identify biological components in proteomics and metabolomics. LC-MS data can be difficult to analyze manually given its amount and complexity. Therefore, we need specialized software that can analyze high-throughput LC-MS data quickly and accurately.
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<ins>**Why use OpenMS**</ins>
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OpenMS in recent times has been expanded to support a wide variety of mass spectrometry experiments. To design your analysis solution, [contact the OpenMS team](https://openms.de/communication/) today.
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```
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To use OpenMS effectively, an understanding of chromatography and mass spectrometry is required as many of the algorithms are based on these techniques.
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To use OpenMS effectively, an understanding of chromatography and mass spectrometry is required as many of the algorithms are based on these techniques.
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This section provides a detailed explanation on LC and MS, and how they are combined to identify and quantify substances.
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Liquid chromatography (LC)
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==========================
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Chromatography is a technique used by life scientists to separate molecules based on a specific physical or chemical property.
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Chromatography is a technique used by life scientists to separate molecules based on a specific physical or chemical property.
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<divclass="admonition video">
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<pclass="admonition-title">**Video**</p>
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For more information on chromatography, [view this video](https://timms.uni-tuebingen.de:/tp/UT_20141028_001_cpm_0001?t=210.00).
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</div>
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There are many types of chromatography, but this section focuses on LC as it is widely used in proteomics and metabolomics.
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There are many types of chromatography, but this section focuses on LC as it is widely used in proteomics and metabolomics.
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LC separates molecules based on a specific physical or chemical property by mixing a sample containing the molecules of interest (otherwise known as **analytes**) in a liquid solution.
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## Key components of LC
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An LC setup is made up of the following components:
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-**A liquid solution**, known as the **mobile phase**, containing the analytes.
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-**A liquid solution**, known as the **mobile phase**, containing the analytes.
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-**A pump** which transports the liquid solution.
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-**A stationary phase** which is a solid, homogeneous substance.
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-**A column** that contains the stationary phase.
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-**A column** that contains the stationary phase.
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-**A detector** that plots the time it takes for the analyte to escape the column (retention time) against the analyte's concentration. This plot is called a **chromatogram**.
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Refer to the image below for a diagrammatic representation of an LC setup.
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Refer to the image below for a diagrammatic representation of an LC setup.
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## How does LC work?
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The liquid solution containing the analytes is pumped through a column that is attached to the stationary phase. Analytes are separated based on how strongly they interact with each phase. Some analytes will interact strongly with the mobile phase while others will be strongly attracted to the stationary phase, depending on their physical or chemical properties. The stronger an analyte's attraction is to the mobile phase, the faster it will leave the column. The time it takes for an analyte to escape from the column is called the analyte's {term}`retention time`. As a result of their differing attractions to the mobile and stationary phases, different analytes will have different retention times, which is how separation occurs.
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The liquid solution containing the analytes is pumped through a column that is attached to the stationary phase. Analytes are separated based on how strongly they interact with each phase. Some analytes will interact strongly with the mobile phase while others will be strongly attracted to the stationary phase, depending on their physical or chemical properties. The stronger an analyte's attraction is to the mobile phase, the faster it will leave the column. The time it takes for an analyte to escape from the column is called the analyte's {term}`retention time`. As a result of their differing attractions to the mobile and stationary phases, different analytes will have different retention times, which is how separation occurs.
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The retention times for each analyte are recorded by a detector. The most common detector used is the mass spectrometer, which we discuss later. However, other detection methods exist, such as:
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## High performance liquid chromatography (HPLC)
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HPLC is the most commonly used technique for separating proteins and metabolites. In HPLC, a high-pressured pump is used to transport a liquid (solvent) containing the molecules of interest through a thin capillary column. The stationary phase is ‘packed’ into the column.
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HPLC is the most commonly used technique for separating proteins and metabolites. In HPLC, a high-pressured pump is used to transport a liquid (solvent) containing the molecules of interest through a thin capillary column. The stationary phase is ‘packed’ into the column.
Copy file name to clipboardExpand all lines: docs/manual/contribute.md
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## Reporting Bugs and Issues
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A list of known issues in the current OpenMS release can be found [here](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/known_dev_bugs.html).
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A list of known issues in the current OpenMS release can be found [here](https://abibuilder.cs.uni-tuebingen.de/archive/openms/Documentation/nightly/html/known_dev_bugs.html).
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Please check if your OpenMS version matches the current version and if the bug has already been reported.
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In order to report a new bug, please create a [GitHub issue](manual/contribute.md#Write and Label GitHub Issues) or [contact us](/about/communication.md).
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