{"id":44257481,"url":"https://github.com/compomics/ms-lims","last_synced_at":"2026-02-10T16:35:49.347Z","repository":{"id":30427343,"uuid":"33980301","full_name":"CompOmics/ms-lims","owner":"CompOmics","description":"Mass spectrometry based proteomics information management system.","archived":false,"fork":false,"pushed_at":"2022-06-21T00:50:44.000Z","size":17055,"stargazers_count":2,"open_issues_count":6,"forks_count":1,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-09-10T05:09:49.201Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Java","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/CompOmics.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE-2.0.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2015-04-15T07:46:30.000Z","updated_at":"2022-03-24T15:10:52.000Z","dependencies_parsed_at":"2022-09-12T18:52:41.513Z","dependency_job_id":null,"html_url":"https://github.com/CompOmics/ms-lims","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/CompOmics/ms-lims","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fms-lims","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fms-lims/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fms-lims/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fms-lims/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/CompOmics","download_url":"https://codeload.github.com/CompOmics/ms-lims/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/CompOmics%2Fms-lims/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29307917,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-10T16:09:25.305Z","status":"ssl_error","status_checked_at":"2026-02-10T16:08:52.170Z","response_time":65,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-02-10T16:35:48.657Z","updated_at":"2026-02-10T16:35:49.333Z","avatar_url":"https://github.com/CompOmics.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ms-lims\n![logo](http://genesis.ugent.be/uvpublicdata/ms-lims/ms-lims_logo.png) \n\n * [Project Description](#project-description)\n * [Downloads](#downloads)\n * [Usage](#usage)\n * [Related Projects](#related-projects)\n * [Project Support](#project-support)\n\n----\n\n## Project Description\n\nThe ms_lims project provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.\n\nMS-based proteomics produces large amounts of mass spectra that require processing, identification and possibly quantification before interpretation can be undertaken. High-throughput studies require automation of these various steps, and management of the data in association with the results obtained. We here present ms_lims, a freely available, open-source system based on a central database to automate data management and processing in MS-driven proteomics analyses.\n\n### Citation\n*Helsens, K., Colaert, N., Barsnes, H., Muth, T., Flikka, K., Staes, A., Timmerman, E., Wortelkamp, S., Sickmann, A., Vandekerckhove, J., et al. (2010). ms_lims, a simple yet powerful open source LIMS for mass spectrometry-driven proteomics. Proteomics epub ([pid: 20058248](http://www.ncbi.nlm.nih.gov/pubmed/20058248)).*\n\n[Go to top of page](#ms-lims)\n\n----\n\n## Downloads\nDownload ms-lims 7.7.7 [here](http://genesis.ugent.be/uvpublicdata/ms-lims/ms-lims-7.7.7.zip). \n\n[Go to top of page](#ms-lims)\n\n----\n\n## Usage\n * The zip file contains the *ms-lims* jar file and all the libraries needed to run the tool. *Double clicking this resulting jar file will start ms-lims.*\n * Download the manual [here](http://genesis.ugent.be/uvpublicdata/ms-lims/ms_lims_manual.pdf).\n * Download the database schema [here](http://genesis.ugent.be/uvpublicdata/ms-lims/schema_7.6.png).\n * Check out the [release notes](https://github.com/compomics/ms-lims/wiki/ReleaseNotes) and [database updates](https://github.com/compomics/ms-lims/wiki/DatabaseUpdates) in the [wiki](https://github.com/compomics/ms-lims/wiki) section.\n\n### Troubleshooting\nPlease report any issues or requests in the [issues section](https://github.com/compomics/ms-lims/issues). We will attempt to come up with a solution as soon as possible.\n\n[Go to top of page](#ms-lims)\n\n----\n\n## Related Projects\nMs-lims makes use of [compomics-utilities](http://code.google.com/p/compomics-utilities).\n\nYou might also find some of the following projects interesting: [Peptizer](http://code.google.com/p/peptizer),\n[dbtoolkit](https://github.com/compomics/dbtoolkit),\n[ms-lims](http://code.google.com/p/ms-lims),\n[Rover](http://code.google.com/p/compomics-rover) and\n[PeptideShaker](http://code.google.com/p/peptide-shaker)\n\n[Go to top of page](#ms-lims)\n\n----\n\n## Project Support\n\nThe ms-lims project is grateful for the support by:\n\n| Compomics | VIB | Ghent University|\n|:--:|:--:|:--:|\n| [![compomics](http://genesis.ugent.be/uvpublicdata/image/compomics.png)](http://www.compomics.com) | [![vib](http://genesis.ugent.be/uvpublicdata/image/vib.png)](http://www.vib.be) | [![](http://genesis.ugent.be/uvpublicdata/image/ugent.png)](http://www.ugent.be/en) |\n\n[Go to top of page](#rover)\n\n----\n\n| IntelliJ | Netbeans | Java | Maven |\n|:--:|:--:|:--:|:--:|\n| [![intellij](http://genesis.ugent.be/uvpublicdata/image/icon_IntelliJIDEA.png)](https://www.jetbrains.com/idea/) | [![netbeans](https://netbeans.org/images_www/visual-guidelines/NB-logo-single.jpg)](https://netbeans.org/) | [![java](http://genesis.ugent.be/uvpublicdata/image/java.png)](http://java.com/en/) | [![maven](http://genesis.ugent.be/uvpublicdata/image/maven.png)](http://maven.apache.org/) |\n\n[Go to top of page](#ms-lims)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcompomics%2Fms-lims","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fcompomics%2Fms-lims","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fcompomics%2Fms-lims/lists"}