List of mzML parsers in different programming languages

[MatthewThe]

As discussed at the HUPO Busan Bioinformatics Hub, it would be great to compile a list of all the available mzML (and mzMLb?) parsers for different programming languages.

Off the top of my head and a quick google search I came up with the following:

Python:

• pyteomics (reading): https://github.com/levitsky/pyteomics
• pymzml (reading): https://github.com/pymzml/pymzML
• psims (writing): https://github.com/mobiusklein/psims

C++:

• proteowizard (reading+writing): https://github.com/ProteoWizard/pwiz
• OpenMS (reading+writing): https://github.com/OpenMS/OpenMS
• MSToolkit (reading+writing): https://github.com/mhoopmann/mstoolkit

C#:

• PSI-interface (reading): https://github.com/PNNL-Comp-Mass-Spec/PSI-Interface

Java:

• jmzml (reading+writing): https://github.com/PRIDE-Utilities/jmzml
• jmzReader (reading): https://github.com/PRIDE-Utilities/jmzReader
• jimzMLParser (reading): https://github.com/AlanRace/jimzMLParser
• one of the developers of MSFragger suggested that they could extract a standalone library

R:

• mzR (reading): https://github.com/sneumann/mzR

Ruby:

• mspire (reading+writing): https://github.com/princelab/mspire

Rust:

• mzdata (reading): https://github.com/mobiusklein/mzdata

[hechth]

I actually started working on a similar overview some time ago, happy to share it here: https://drive.google.com/file/d/1zCWSxupRBK8igHyGoXvENJ5SJQL86Kx_/view?usp=drive_link

[RalfG]

Some others:

Python:

• tdf2mzml (writing): https://github.com/mafreitas/tdf2mzml
• timsconvert (writing): https://github.com/gtluu/timsconvert

---

No interactions with mzML (yet)

Rust:

• timsrust https://github.com/mannlabs/timsrust

R:

• https://github.com/MatteoLacki/timsr

Python:

• https://github.com/MatteoLacki/timspy

[edeutsch]

We should add these to the https://psidev.info/mzML page
But also add a comment for each about its current state, if it is currently maintained or not

[Mailaender]

I just submitted eclipse/chemclipse#1863 so that ChemClipse and @OpenChrom support mzML read/write for MSD and DAD chromatograms and single mass spectra. There are still things to do for high res and MS/MS though.