Abstract
Proteomics laboratories and proteomics service facilities produce a large volume of data that originate from diverse sources, involve the participation of several members of the lab, and are communicated to clients and collaborators of the laboratory. Laboratory information management systems (LIMS) play a key role in collating and tracking the flow of data through the laboratory. The cost of off-the-shelf LIMS systems can be significant and compounded by further customization, development, and installation costs. Fields that employ rapidly changing technologies in support of research require information management that is stringent and secure, but also must be adaptable. We have developed an open-source scientific data management system for proteomics that is capable of acting as a stand-alone LIMS system, or working in conjunction with other LIMS systems. We support sample processing workflow, protocols, and datasets generated by LC-ESI, LC-MALDI, MALDI, 1D-GELS, 2D-GELS, and 2D-gel image analysis. The workflow supports input from existing data analysis and allows batch analysis of proteomics data to be queued to search engines and other tools. It supports extensive data curation, has a simple Web browser interface that allows tiered, secure access to data and functions, and also allows export of data from individual spectra up to full project files. The source code is available from Proteomecommons.org. Installation of the software can be performed through https://www.prime-sdms.org/main.htm.