Rapid QC-MS: Interactive Dashboard for Synchronous Mass Spectrometry Data Acquisition Quality Control

Area of Science:

• Analytical Chemistry
• Biotechnology
• Data Science

Background:

• High-throughput untargeted liquid chromatography-coupled tandem mass spectrometry (LC-MS/MS) workflows are crucial for biological research.
• Manual quality control (QC) of LC-MS/MS data, including the evaluation of analytical standards, is a significant bottleneck, consuming substantial time and resources.
• Existing methods for real-time data quality assessment are often inefficient and prone to inaccuracies.

Purpose of the Study:

• To develop an automated and interactive dashboard, Rapid QC-MS, for efficient assessment of LC-MS/MS data quality.
• To streamline the process of evaluating analytical controls and identifying low-integrity specimens in high-throughput LC-MS/MS experiments.
• To provide researchers with a user-friendly tool for monitoring instrument performance and data integrity in near real-time.

Main Methods:

• Development of an open-source, interactive dashboard (Rapid QC-MS) using Python libraries and established MS analysis software.
• Integration of automated quality control metrics including instrument sensitivity, retention time shifts, and mass accuracy drift.
• Implementation of local data processing with optional remote syncing (Google Drive) and semiautonomous alerting via messaging applications.

Main Results:

• Rapid QC-MS provides near real-time, browser-viewable quality control results minutes after data file generation.
• The dashboard offers interactive visualizations to detect both acute deviations and gradual drifts in performance metrics over various time scales.
• The system successfully integrates with Thermo Orbitrap workflows, offering a configurable and adaptable solution for diverse LC-MS/MS applications.

Conclusions:

• Rapid QC-MS significantly reduces the time and effort required for manual data curation in untargeted LC-MS/MS workflows.
• The automated quality control system enhances the accuracy and reliability of data integrity assessment.
• Rapid QC-MS provides a fast, straightforward, and open-source solution for collecting high-quality untargeted LC-MS/MS data.