bookmark ms_lims A freely available, open-source system based on a central database to automate data management and processing in mass spectrometry driven proteomics analyses. ms-lims is mainly designed to automate data flow in the high-throughput proteomics lab. Taking spectrum files from a variety of pluggable file formats, it transforms these to the Mascot Generic Format and stores them in the database, retaining LC information if present, and also allowing additional information to be stored for each individual LC run. Another part allows the retrieval of the stored spectra in mergefiles of arbitrary size. These can then be submitted to a search engine, eg. Mascot from Matrix Science. Subsequently, the results of these searches can be parsed and stored in a relational database structure for future reference.