FAQ

This section provides a list of frequently asked questions concerning usage, installation, and development of Rapid-QC-MS.

If you don’t find an answer to your question, please feel free to contact us or submit an issue on GitHub.

General

What instrument vendors are supported?

Rapid-QC-MS was designed to be vendor-agnostic. It parses acquisition sequences based on instrument vendors, and converts data files from closed vendor format to open mzML format before processing.

However, with this initial release (v1.0.0), only Thermo Fisher instruments are fully supported.

If you would like to help us develop support for Agilent, Bruker, Sciex, or Waters acquisition sequences and data files, please contact us by sending an email to brian.defelice@czbiohub.org.

Is MacOS supported?

Yes! Rapid-QC-MS is a Python package, so it can be installed and used on any operating system that runs Python.

Once you install Rapid-QC-MS on your Mac, you have the ability to sign in to your workspace and monitor your QC jobs.

However, you cannot set up QC jobs on MacOS. This is because the processing workflow depends on MSConvert and MS-DIAL, both of which are only supported for Windows.

How is quality control performed?

In short, Rapid-QC-MS monitors active instrument runs and quantifies internal standards in each sample following acquisition.

The RT and m/z of all internal standards found in a sample are compared to their corresponding library values. Rapid-QC-MS also compares each internal standard’s RT to the in-run average RT, and counts the number of missing internal standards in a sample.

If total missing internal standards, absolute RT, in-run RT, or accurate mass fall outside user-defined cutoffs, the sample is deemed a “QC fail”. If the criteria are close to a fail, a “QC warning” is issued instead.

You can read more about the processing workflow here.

Is this software only for untargeted?

No, it will work for targetted as well.

Installation

How can I uninstall Rapid-QC-MS not installed with a virtual environment?

To uninstall Rapid-QC-MS outside of a virtual environment, simply open a terminal window and type:

py -m pip uninstall rapid-qc-ms

You will be prompted to confirm by entering Y, and then the package will be uninstalled.

Is my workspace deleted if I uninstall or re-install Rapid-QC-MS?

Uninstalling Rapid-QC-MS does NOT delete workspace data such as QC results and settings for your instrument. These must be removed manually.

To delete all workspace data, you can type:

rmdir /s C:\Users\<YOUR-USERNAME-HERE>\AppData\Local\Programs\python\<PYTHON-VERSION>\lib\site-packages\rapidqcms

Note: The <PYTHON-VERSION> will be denoted as python39 if you have Python 3.9, or python310 if you have Python 3.10, for example.

If you installed Rapid-QC-MS in a virtual environment, then the relevant command is:

rmdir /s <path-to-venv-folder>\lib\site-packages\rapidqcms

Or, if you feel safer to navigate to the folder and delete it yourself, simply paste the above directory into your File Explorer and delete the folders.

Setup

Why isn’t MSConvert being detected by Rapid-QC-MS?

If MSConvert is not being detected, try each of the following and see if it solves the problem:

  • Refresh the page in the browser
  • Restart the computer
  • Reinstall MSConvert
  • Reinstall .NET Framework

Why isn’t MS-DIAL being detected by Rapid-QC-MS?

If MS-DIAL isn’t being located, you might have provided Rapid-QC-MS the wrong folder (or you might not have provided the location at all).

  • Check to make sure that the directory you have provided in Settings > MS-DIAL Configurations isn’t a folder containing the MS-DIAL folder.

  • Once you have saved a new MS-DIAL directory, refresh the page in your browser and try again.

If this doesn’t solve the problem, check to make sure MsdialConsoleApp.exe exists in your MS-DIAL folder.

  • If it doesn’t, you may have a newer version of MS-DIAL. Go to the MS-DIAL website and download any one of the v4 releases.

If all else fails, try to rename your folder to something with no spaces such as MS-DIAL.

Usage

Is an “instrument run” the same as a “QC job”?

Yes. In the context of this app, both terms can be used interchangeably.

Something went wrong. How do I “reset” the app?

As a general rule of thumb, if the UI freezes or produces a bug, try refreshing the page in your browser.

If that doesn’t work, try restarting the app by 1) closing the Command Prompt window and 2) launching a new instance using rapidqcms.

What happens if I refresh / close the app during an active instrument run?

Nothing! The acquisition listener process runs in the background, so it will not be interrupted.

What happens if I restart rapidqcms from the Command Prompt during an active instrument run?

If the Rapid-QC-MS process was interrupted during an instrument run, perform the following steps:

1. Restart Rapid-QC-MS

Do this by entering rapidqcms in a Command Prompt window.

2. Select the instrument run from the table

Every time you select a run, Rapid-QC-MS will check to see if the run is active. If the run is active, then it will check to see if the listener process is still running, and restart it as needed.

How can I delete a job and start over?

Follow the steps below:

  1. Select the instrument run from the table
  2. Click the “Delete Job” button
  3. Confirm and wait for the alert to disappear
  4. Refresh the page

When you refresh the page, the instrument run should no longer appear on the dashboard.