Tutorials

We have a couple of tutorials and guides to offer, this page will lead you to them:

with python

• read mzQC:
• write mzQC:
• demo video

with R

• rmzQC
• PTXQC demo

Validation

If you have many mzQC files to validate, or the validation API is temporaily unreachable, you can set up your own validation process without much effort!

Container

The container solution is the least effort, but requires you have the singularity container engine installed.

Local Installation of pymzqc

This solution requires you to install pymzqc. In most cases it will be as easy as simply pip install pymzqc. For all the latest instructions on installation of pymzqc and validation, see its repository.

JSON

If you are new to JSON or file formats (with JSON), the next few links should provide you with an overview:

• JSON (by W3C)
• JSON (by mozilla)
• File format schemas with JSON
• JSON crash course (by freecodecamp)

Ontologies

Ontologies also known as controlled vocabularies are used in mzQC to manage metric definitions and metric value content. Here is a list of links and documents that should help you out in case you want to know more.

• Ontologies are powerful tools, we mostly use them as controlled vocabularies
• The W3C has a bit broader explanation of ontologies
• Visit the HUPO-PSI webpage for more information on CV use in different settings.
• Browse our controlled vocabulary terms on OLS
• If you want to start with the foundations and get ambitious here are the resources from protege for ontology development
• Luckily, we have all the relevant metrics and terms in PSI-MS CV (_{so no Ontology Dowsing necessary})