Rapid QC-MS:\nInteractive Dashboard for Synchronous\nMass Spectrometry Data Acquisition Quality Control

Consistently collecting high-quality liquid chromatography-coupled\ntandem mass spectrometry (LC-MS/MS) data is a time-consuming hurdle\nfor untargeted workflows. Analytical controls such as internal and\nbiological standards are commonly included in high-throughput workflows,\nhelping researchers recognize low-integrity specimens regardless of\ntheir biological source. However, evaluating these standards as data\nare collected has remained a considerable bottleneckin both\nperson-hours and accuracy. Here we present Rapid QC-MS, an automated,\ninteractive dashboard for assessing LC-MS/MS data quality. Minutes\nafter a new data file is written, a browser-viewable dashboard is\nupdated with quality control results spanning multiple performance\ndimensions such as instrument sensitivity, in-run retention time shifts,\nand mass accuracy drift. Rapid QC-MS provides interactive visualizations\nthat help users recognize acute deviations in these performance metrics,\nas well as gradual drifts over periods of hours, days, months, or\nyears. Rapid QC-MS is open-source, simple to install, and highly configurable.\nBy integrating open-source Python libraries and widely used MS analysis\nsoftware, it can adapt to any LC-MS/MS workflow. Rapid QC-MS runs\nlocally and offers optional remote quality control by syncing with\nGoogle Drive. Furthermore, Rapid QC-MS can operate in a semiautonomous\nfashion, alerting users to specimens with potentially poor analytical\nintegrity via frequently used messaging applications. Initially developed\nfor integration with Thermo Orbitrap workflows, Rapid QC-MS offers\na fast, straightforward approach to help users collect high-quality\nuntargeted LC-MS/MS data by eliminating many of the most time-consuming\nsteps in manual data curation. Download for free: https://github.com/czbiohub-sf/Rapid-QC-MS.