iMonDB

The iMonDB (Instrument MONitoring DataBase) tool suite consists of a highly efficient database structure and associated software tools to automatically extract, store, and manage mass spectrometry instrument parameters from raw data files.

Instrument parameters give a detailed account on the operation of a mass spectrometer, which can subsequently give insight into the observations in the mass spectral data. The advantage of instrument information at the lowest level is the high sensitivity to detect emerging defects in a timely fashion. The iMonDB enables the monitoring of instrument parameters over a considerable time period, which fosters an additional approach to mass spectrometry quality control.

The iMonDB tool suite consists of the following components:

• iMonDB MySQL database: a highly optimized database structure to store instrument parameters
• iMonDB Collector: a schedulable tool to keep the iMonDB up to date by automatically storing new instrument parameters in the database
• iMonDB Viewer: a tool to visualize the evolution of individual instrument parameters over time
• iMonDB Core: a high-level Java API for use by developers who wish to include instrument monitoring capabilities in their own software

Currently only the extraction of instrument parameters for Thermo Scientific instruments is supported (full list of supported instruments). However, care has been taken to ensure that the database structure accomodates a wide range of instrument models and allows for the integration with other mass spectrometer vendors as well. To request the inclusion of additional instrument models and/or vendors, please contact us by creating an issue, including representative raw data file(s).

The various iMonDB implementations are released as open source under the permissive Apache 2.0 license. If you use iMonDB as part of your work, please cite the following publication:

• Bittremieux, W., Willems, H., Kelchtermans, P., Martens, L., Laukens, K., and Valkenborg, D. iMonDB: Mass spectrometry quality control through instrument monitoring. Journal of Proteome Research (2015). doi:10.1021/acs.jproteome.5b00127

For installation instructions, detailed documentation, and usage examples, please see the documentation.

News

iMonDB Viewer v1.1.2 (09-Oct-2015)

• NEW FEATURE: Browse through property graphs using left/right keys
• NEW FEATURE: Import and export events from/to a csv file
• ENHANCEMENT: Upgrade to iMonDB-core v1.0.5
• ENHANCEMENT: Top bar wraps when resizing to a smaller screen

iMonDB Collector v1.1.2 (07-Apr-2015)

• ENHANCEMENT: Upgrade to iMonDB-core v1.0.5

iMonDB Core v1.0.5 (07-Apr-2015)

• ENHANCEMENT: Support several additional instrument models
• BUGFIX: Fix possible error when using the default instrument reader

For more information see the release notes.

Getting iMonDB

The Downloads section contains the jar executables for the various iMonDB tools. Furthermore, the complete source code is available from this repository through git.

Getting Help

If you have questions or need additional help, you can contact us by creating an issue.

Please let us know your feedback, including error reports, improvement suggestions, new feature requests, and any other things you might want to suggest.

When reporting a bug, please remember to include the log file generated by iMonDB and the JPA log file (using a detailed log level).

The iMonDB is supported by the InSPECtor project.