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The large data set obtained by metabolomics techniques makes a good data storage system essential. This systems should not only store the raw data but also store all the information on the experiment and samples. Such is a system is often called Laboratory Information Management System (LIMS).
Examples of metabolomics LIM systems:
MetaboLIMS
is a web-based, portable, robust, and scalable laboratory information management system designed to meet the production and clinical needs of laboratories involved in metabolomics research. It offers a wide variety of functions such as Compound and Sample Tracking, Electronic Notebook Entry, GANTT Charting, Instrument and Meeting Scheduling, Text Data Entry, Spectral Trace or Image Entry, Automated Analysis and Report Generation, Audit Trail Tracking, Relational Query Searches as well as NMR and MS Spectral Searches. MetaboLIMS is also supplemented with a large database of ~1400 metabolites and unique set of search tools (called BioSpider and PolySearch) to facilitate metabolite annotation and identification. MetaboLIMS employs a customizable modular design, allowing users or administrators the ability to add or remove LIMS GUI components and lists as needed. MetaboLIMS uses a number of advanced web-building technologies, including HTML, CSS, XML, Javascript, Java Servlet and JSP, as well as MYSQL for its backend database engine. MetaboLIMS is freely available and can be easily installed as a local web server on any Windows and Unix operating platform, making it ideal for labs with limited budget. link
SetupX and BinBase
Two databases developed in the Fiehn laboratory steer laboratory workflows, process mass spectrometry raw data and disseminate result data. SetupX hosts study design metadata that define the biological objects, treatments and time points of a study as well as experimental metadata such as sample preparation and mass spectrometry methods. Laboratory assistants use SetupX to download and randomize sequence tables for the mass spectrometers. After data acquisition, a relational database system (BinBase) is employed for automated metabolite annotation using a multi-tiered filtering system to retain only high quality and consistent metabolite peaks. Results are exported back to SetupX for downloads. link
Metabolomics LIMS
This system is developed by Core Informatics. Metabolomics labs can benefit from the increased efficiency, data integrity and security, communication, and collaboration provided by the Core LIMS. The system assists users performing metabolomics profiling studies in analyzing large amounts of multivariate chromatography and spectrometry data to determine significant patterns. This can lead to the discovery of methods of earlier and more accurate diagnoses of disease, and the creation of more effective treatments. Each data point collected by the Core LIMS is associated with the instrument and operator it was generated from, as well as any protocol(s) it is related to. This provides traceability for audits as well as allowing analysts to find where an irregularity or sample contamination occurred.
The LIMS supports in-vitro and in-vivo studies, and can track data for compounds, metabolites, or any other object a lab gathers data on. It facilitates data comparison across lots, studies, workflows, projects, etc. The Core system directly interfaces with instruments used in chromatography, electrophoresis, mass spectrometry, and nuclear magnetic resonance (NMR) spectroscopy. link
Examples of metabolomics LIM systems:
MetaboLIMS
is a web-based, portable, robust, and scalable laboratory information management system designed to meet the production and clinical needs of laboratories involved in metabolomics research. It offers a wide variety of functions such as Compound and Sample Tracking, Electronic Notebook Entry, GANTT Charting, Instrument and Meeting Scheduling, Text Data Entry, Spectral Trace or Image Entry, Automated Analysis and Report Generation, Audit Trail Tracking, Relational Query Searches as well as NMR and MS Spectral Searches. MetaboLIMS is also supplemented with a large database of ~1400 metabolites and unique set of search tools (called BioSpider and PolySearch) to facilitate metabolite annotation and identification. MetaboLIMS employs a customizable modular design, allowing users or administrators the ability to add or remove LIMS GUI components and lists as needed. MetaboLIMS uses a number of advanced web-building technologies, including HTML, CSS, XML, Javascript, Java Servlet and JSP, as well as MYSQL for its backend database engine. MetaboLIMS is freely available and can be easily installed as a local web server on any Windows and Unix operating platform, making it ideal for labs with limited budget. link
SetupX and BinBase
Two databases developed in the Fiehn laboratory steer laboratory workflows, process mass spectrometry raw data and disseminate result data. SetupX hosts study design metadata that define the biological objects, treatments and time points of a study as well as experimental metadata such as sample preparation and mass spectrometry methods. Laboratory assistants use SetupX to download and randomize sequence tables for the mass spectrometers. After data acquisition, a relational database system (BinBase) is employed for automated metabolite annotation using a multi-tiered filtering system to retain only high quality and consistent metabolite peaks. Results are exported back to SetupX for downloads. link
Metabolomics LIMS
This system is developed by Core Informatics. Metabolomics labs can benefit from the increased efficiency, data integrity and security, communication, and collaboration provided by the Core LIMS. The system assists users performing metabolomics profiling studies in analyzing large amounts of multivariate chromatography and spectrometry data to determine significant patterns. This can lead to the discovery of methods of earlier and more accurate diagnoses of disease, and the creation of more effective treatments. Each data point collected by the Core LIMS is associated with the instrument and operator it was generated from, as well as any protocol(s) it is related to. This provides traceability for audits as well as allowing analysts to find where an irregularity or sample contamination occurred.
The LIMS supports in-vitro and in-vivo studies, and can track data for compounds, metabolites, or any other object a lab gathers data on. It facilitates data comparison across lots, studies, workflows, projects, etc. The Core system directly interfaces with instruments used in chromatography, electrophoresis, mass spectrometry, and nuclear magnetic resonance (NMR) spectroscopy. link
MetLIMS
MetLIMS is part of the MetIQ software package of Biocrates. MetIQ provides you with a solution for the complete analytical process of targeted metabolomics, from project setup to biological interpretation of measurement data. MetIQ should work with several laboratory environments. link