SimExTargId: a comprehensive package for real-time LC-MS data acquisition and analysis.

Area of Science:

• Metabolomics
• Bioinformatics
• Analytical Chemistry

Background:

• Liquid chromatography mass spectrometry (LC-MS) is crucial for analyzing small molecules in biofluids.
• Untargeted metabolomic analysis requires robust and automated data processing pipelines.
• Existing workflows can be complex and time-consuming, necessitating streamlined solutions.

Purpose of the Study:

• To introduce SimExTargId, an open-source R package for autonomous metabolomic data analysis.
• To provide real-time observation and quality control during LC-MS experimental runs.
• To facilitate efficient and accurate identification of metabolites in complex biological samples.

Main Methods:

• SimExTargId integrates vendor-independent format conversion (ProteoWizard).
• It employs xcms and CAMERA for peak picking and MetMSLine for pre-processing.
• Includes covariate-based statistical analysis and email notifications for instrument errors.

Main Results:

• The package enables simultaneous, fully automated, and optionally multi-threaded data processing.
• Provides two Shiny applications: targetId for real-time MS2 target identification and peakMonitor for targeted metabolite monitoring.
• Enhances the efficiency and reliability of untargeted metabolomic data analysis.

Conclusions:

• SimExTargId offers a comprehensive, automated solution for LC-MS metabolomic data analysis.
• The package improves experimental run observation and data quality control.
• It is publicly available, promoting accessibility and further development in the field.