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Listening to your mass spectrometer: An open-source toolkit to visualize mass spectrometer data
Abed Pablo1,2, Andrew N Hoofnagle1,2, Patrick C Mathias1,2
1Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA, USA.
Journal of Mass Spectrometry and Advances in the Clinical Lab
|January 14, 2022
Summary
We created open-source tools to manage LC-MS/MS data and quality control. This enhanced data review, improving the SMACK algorithm
Area of Science:
- Clinical Chemistry
- Analytical Chemistry
- Biotechnology
Background:
- Developed open-source tools for collecting and monitoring LC-MS/MS data.
- Includes a database and visualization component for quality control parameters.
Purpose of the Study:
- To create a customizable web-based dashboard for LC-MS/MS instrument performance monitoring.
- To improve the efficiency of data review and results using quality control algorithms.
Main Methods:
- Utilized Python and standard libraries to parse XML files from clinical runs.
- Stored parsed data in a three-table database.
- Developed an interactive data visualization tool with 5 interchangeable visualizations.
Main Results:
- Assessed quality control parameter performance using histogram visualization.
- The SMACK algorithm showed a 1.7% increase in flags and a 7.1% decrease in false positive flags.
- Improved SMACK algorithm performance, allowing staff to focus on critical QC failures.
Conclusions:
- Developed a web-based dashboard for monitoring LC-MS/MS assay instrument performance.
- The platform enables proactive instrument maintenance, reducing laboratory downtime.
- The system is customizable for various laboratory instruments.
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