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Mass spectrometry based proteomics information management system.
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Project Description

The ms_lims project provides a lightweight, portable yet production-grade solution for managing mass spectrometry based proteomics data.

MS-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.


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).

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Download ms-lims 7.7.7 here.

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  • 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.
  • Download the manual here.
  • Download the database schema here.
  • Check out the release notes and database updates in the wiki section.


Please report any issues or requests in the issues section. We will attempt to come up with a solution as soon as possible.

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Related Projects

Ms-lims makes use of compomics-utilities.

You might also find some of the following projects interesting: Peptizer, dbtoolkit, ms-lims, Rover and PeptideShaker

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Project Support

The ms-lims project is grateful for the support by:

Compomics VIB Ghent University
compomics vib ugent

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