Running the demo • MetabolomiQCsR

Download and compilation

Make sure to revisit the prerequisites on the front page.

First download the repository to somewhere convenient (here /opt).

cd /opt
sudo git lfs clone https://github.com/stanstrup/QC4Metabolomics.git
cd QC4Metabolomics
sudo chmod +x ./setup/*.sh

Now you need to build the image which requires downloading many R packages (a pre-compiled image is not currently available) and will take a while. This will also start the demo.

docker compose --file docker-compose_demo.yml up --build --force-recreate

Getting started with the demo

You can now open the demo in your browser by visiting localhost. It might take a few minutes before it can load though, since the database needs to be initialized on first load.

You will also see that no plots appear. This is because no compounds to analyze has been defined.

First click the Contaminants tab. If no plot appears go get a coffee and come back and reload the page (it will look for new compounds every 1 min and then analyze the data). The plot is available when the system has analyzed the demo files. Once a plot appears you can try to change the “Minimum intensity in any sample” (for example to 10³). Now you can see which are the most common contaminants.

Track specific compounds

Now we want to make the tracking of specific analytes work. So go to the Track compounds –> Compound settings tab. Now we fill in the data to track Tryptophan in both modes.
These are the settings you need:

Compound name	Instrument	Mode	m/z	RT1
L-Tryptophan	Sold	pos	188.0706	2.55
L-Tryptophan	Sold	neg	203.0826	2.55

Click “Submit” when you have filled the form and repeat for the second compound/mode.

When you are done it should look like this:

Settings to track tryptophan

After some minutes you should be able reload the browser and see the data for tryptophan in the “Track compounds” -> “Compound stats” tab.

Enabling email warnings

By default the e-mail warnings are off, since you need to supply your own email server settings to send e-mails.
You can use GMail or any other SMTP server to send emails. If you use GMail you need to create an “app password”, which can be done in your GMail account, and not use your regular GMail password.

Once you have create your password you need to edit the settings for the “Warner module”. You do that by opening the file settings_demo.env and scrolling down to the section “module: Warner”. First you enable the module by setting QC4METABOLOMICS_module_Warner_enabled to TRUE.

QC4METABOLOMICS_module_Warner_enabled=TRUE

Next you need to set your credentials and server. Below is an example where EMAIL_SENDER and YOUR_USER would be your email address for the account that sends the emails and EMAIL_RECEIVER would be the address of the email that should receive the emails (can be the same as the sender). The password is the account password or in the case of GMail the “app password”. Below are the settings needed for GMail.

QC4METABOLOMICS_module_Warner_email_from=EMAIL_SENDER
QC4METABOLOMICS_module_Warner_email_to=EMAIL_RECEIVER
QC4METABOLOMICS_module_Warner_email_user=YOUR_USER
QC4METABOLOMICS_module_Warner_email_password=YOUR_PASSWORD
QC4METABOLOMICS_module_Warner_email_host=smtp.gmail.com
QC4METABOLOMICS_module_Warner_email_port=587
QC4METABOLOMICS_module_Warner_email_use_ssl=TRUE

You should now stop QC4Metabolomics (ctrl + C) and start it again using:

docker compose --file docker-compose_demo.yml up --build --force-recreate

Next go to the “Warning rules” tab and setup some rules. Any file that matches any of the rules will trigger an email. The emails are send as soon as a matching file is found, but in bulk for all newly found files and only once per file.

The rules only apply to files from a specific Instrument, as extracted from the filename. Next you need to select which statistic to monitor. Usually the most relevant statistics are the m/z deviation from the expected (mz_dev_ppm), the retention time deviation from the expected in minutes (rt_dev) and the apex intensity (maxo).
You then choose the operator meaning the comparison to be done. “Greater than” (>) would be typical. Then the Value to compare the statistic to needs to be chosen and finally it should be decided if the absolute value of the Value is to be considered instead of the raw (signed) value.

To check the system with the demo you could try these settings that will trigger on all files where the m/z deviation is more than 30 ppm.

Rule Name	Instrument	Statistics	Operator	Value	Use absolute value?
PPM out of range	Sold	mz_dev_ppm	>	30	TRUE

Settings to trigger warnings

Backups

QC4Metabolomics automatically backs up your database to the folder backups. Settings for the backup frequency can be found at in the DB backup section in settings_demo.env.

Refer to “Running your own system” for more explanation of settings.