Welcome to the OpenMS NuXL App, a web application for the NuXL protein-nucleic acid search engine built using OpenMS and pyOpenMS.
website: https://abi-services.cs.uni-tuebingen.de/nuxl/
NuXL is a dedicated software package designed for the analysis of XL-MS (cross-linking mass spectrometry) data obtained from UV and chemically crosslinked protein–RNA/DNA samples. This powerful tool allows for reliable, FDR-controlled assignment of protein–nucleic acid crosslinking sites in samples treated with UV light or chemical crosslinkers. It offers user-friendly matched spectra visualization, including ion annotations.
Rescoring refers to the post-processing of initial identification results to improve discrimination between correct and incorrect matches by incorporating additional evidence, such as predicted retention time or fragment ion intensities. Such approaches have been shown to increase the identification rate.
👉 With NuXL App users can analyze data with NuXL search engine, run rescoring pipeline, and result interpretation with cross-link aware visualization.
- Reference:
- NuXL search engine: Welp, L. M., Wulf, A., Chernev, A., Horokhovskyi, Y., Moshkovskii, S., Dybkov, O., ... & Urlaub, H. (2025). Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid–protein interaction sites by mass spectrometry. Nucleic Acids Research, 53(15), gkaf727. https://doi.org/10.1093/nar/gkaf727
- NuXL rescore: Siraj, A., Bouwmeester, R., Declercq, A., Welp, L., Chernev, A., Wulf, A., ... & Sachsenberg, T. (2024). Intensity and retention time prediction improves the rescoring of protein‐nucleic acid cross‐links. Proteomics, 24(8), 2300144.https://doi.org/10.1002/pmic.202300144
powered by:
- To get started, download and extract the OpenMS-NuXLApp.zip file from latest successfull action.
- After installation of
OpenMS-NuXLApp.msi, The app can then be launched using the corresponding desktop icon. - Use app in your default browser.
The workspaces for the project will be locally generated in the workspaces-nuxl-app directory, and the analysis will run using local resources.
User can start right away analyzing your data by following the steps below:
On the left side of this page user can define a workspace where all data including uploaded files will be stored. Entering a workspace will switch to an existing one or create a new one if it does not exist yet. In the web app, user can share their results via the unique workspace ID. Be careful with sensitive data, anyone with access to this ID can view access the data.
Upload .mzML. .raw and .fasta files via the File Upload tab. The data will be stored in the workspace. With the online hosted web app, user can upload only one file at a time.
Locally there is no limit in files. However, it is recommended to upload large number of files by specifying the path to a directory containing the files.
Your uploaded files will be shown on the same File Upload page in mzML files and Fasta files tabs. Also user can remove the files from workspace.
Users can download the example files from Load example file tab to current workspace.
Select the .mzML/.raw and .fasta files for analysis, configure user settings including NuXL advanced parameters, and start the analysis using the Run-analysis button.
User can terminate the analysis immediately using the Terminate/Clear button and user can see the real-time log of search engine. Once the analysis completed successfully, the output table will be displayed on the page, along with downloadable links for crosslink identification files for that particular analysis.
Select without FDR-controlled .idXML file from output of NuXL search engine. The name of file pattern is (raw or mzML file_name).idXML. If the NuxL search engine succesfully run, the file will showup here. After including the features start the analysis using the Run-rescoring button.
User can terminate the rescoring analysis immediately using the Terminate/Clear button and User can see the real-time log of rescoring. Once the analysis completed successfully, the comparison PseudoROC curve at CSM-level FDR will generated, and available for download.
Select the experiments with (.mzML) it will extract the identified protein-NA and peptides from NuXL output at 1% CSM-level FDR, available in .idXML files. Optionally, user can do iRT alignment by providing MSFragger library.tsv, with linear or piecewise calibration mode.
User can start the analysis using the Generate Library button. USer can terminate the rescoring analysis immediately using the Terminate/Clear button and User can see the real-time log of spectral library generation.
Here, user can visualize and explore the output of the search engine. All crosslink output files in the workspace are available on the View Results tab.
After selecting any file, user can view the CSMs Table, PRTs Table, PRTs Summary, Crosslink efficiency and Precursor adducts summary.
Users can manage their result files available in workspace with Result files tab.Also Users can upload previously analyzed results files .idXML and .tsv to workspace with Upload result files tab.
Note: Every table and plot can be downloaded, as indicated formats in the side-bar under ⚙️ Settings.
How to upload result files (e.g., from external sources/collaborator) for manual inspection and visualization?
At Upload result files tab, user can upload the results files and can visualize in View Results tab.
In the web app, collaborators can visualize files by sharing a unique workspace ID.
For any inquiries or assistance, please feel free to reach out to us.
