Background The EMBER (East Midlands Breathomics Pathology Node) project is a multi-disciplinary project which aims to discover how breathomics can be used to diagnose cardiorespiratory diseases. In EMBER, data is generated using various analytical chemistry techniques and tools across different remote sites with each technique and site having distinct operational / data handling protocols. While single informatics solutions exist for handling aspects of data management (e.g. data warehousing, tissue tracking), there are no tools which will handle the combined integration of direct chemometric data collection, sample tracking and clinical data from remote sites. Methods We developed and implemented a flexible modular informatics toolkit called LabPipe and used qualitative methods to obtain feedback from users to assess the effectiveness of the tool. Results LabPipe handles analytical chemistry data integration, including real-time notifications to researchers and users, as well as providing a bridge to a data warehouse. The system has been continuously running for a year, with active maintenance to provide performance improvements and to meet new feature requests. User and researcher feedback indicates that the toolkit is stable, reliable and efficient. LabPipe has also reduced the person effort required to maintain data consistency, integrate data and perform quality control checks. Conclusions LabPipe has helped to streamline the flow of data from the clinic to the researchers including notifying users of potential problems with data collection. The modular approach taken to the design of LabPipe has allowed it to be used across multiple studies and enabled different analytical chemistry data formats to be handled effectively.