Rapid-QC-MS

Rapid-QC-MS is an all-in-one solution for automated quality control of liquid chromatography-mass spectrometry (LC-MS/MS) analyses, both during and after data acquisition.

It offers a fast, straightforward approach to ensure collection of high-quality data, allowing for less time investigating raw data and more time conducting experiments.

Developed at the Mass Spectrometry Platform of CZ Biohub San Francisco, Rapid-QC-MS provides a host of key features to streamline high-fidelity untargeted LC-MS/MS analysis, such as:

• Automated and user-defined quality control during data acquisition
• Realtime updates on QC fails in the form of Slack or email notifications
• Interactive data visualization of biological standards - reference and external control samples - and internal standard metrics - retention time, mass accuracy, and intensity across samples
• Google Drive cloud sync and secure, Google-authenticated access to QC results from any device

Requirements

Rapid-QC-MS was designed to run on Windows platforms because of its dependency on MSConvert for vendor format data conversion and MS-DIAL for data processing. However, MacOS users can still use Rapid-QC-MS to monitor / view their instrument run data.

In addition, Rapid-QC-MS requires Python 3.8+ and various Python packages, including:

• Pandas
• SQLAlchemy
• Plotly Dash
• Bootstrap
• Watchdog
• Google API
• Slack API

These are installed automatically during setup.

Note: Installation of Python and various Python packages on MS instrument computers comes at no risk. For extra security and peace of mind, you can opt to install Rapid-QC-MS in a virtual environment. To learn more, please read the installation guide.

Installation and usage

Installing Rapid-QC-MS is easy. Simply open your Terminal or Command Prompt and enter:

py -m pip install rapidqcms

Python dependencies are installed automatically, but dependencies such as MSConvert and MS-DIAL will need to be installed manually.

To start Rapid-QC-MS, simply enter:

rapidqcms

You can also opt to download and install Rapid-QC-MS manually, or in a virtual environment if you prefer. Check out the installation guide for more details.

Example data can be downloaded from metabolomics workbench with supplementary example files (sequence .csv, library .msp, and additional .raw files not published through workbench) available on zenodo.

Supported instrument vendors

Rapid-QC-MS was designed to be a universal, open-source solution for data quality control. Because MSConvert converts raw acquired data into open mzML format before routing it to the data processing pipeline, the package will work seamlessly with data of all vendor formats.

However, Rapid-QC-MS has only been tested extensively on Thermo Fisher mass spectrometers, Thermo acquisition sequences, and Thermo RAW files. As such, it is expected that there may be bugs and issues with processing data of other vendor formats.

If you encounter a bug, please report it by opening an issue on GitHub.

We are open to collaboration! If you would like to help us develop support for Agilent, Bruker, Sciex, or Waters acquisition sequences and data files, please send an email to brian.defelice@czbiohub.org.