Chromatograms from mzXML files

[anani-a-missinou]

Hi dear developers,

We want to use your tools to generate chromatograms for our article.

We have data in mzXML format for which we do not have the constructor files.

It seems that your tool does not support this format. Would it be possible to add it?

thank you

[ethanbass]

Hi,
There is pretty good support for mzXML data in the RaMS package which is what I'm using to parse mzML files currently. It would probably be pretty easy to add mzXML to chromConverter, but it might be just as easy for you to use the mzXML parser in RaMS directly. Maybe you could try RaMS::grabMzxmlData and see if it can read your files?
Thanks and please let me know how it goes.
Ethan

[ethanbass]

@anani-a-missinou Actually, since it's the same function in RaMS that reads mzML and mzXML you should be able to use read_chroms for this and just specify the format as "mzml". e.g. read_chroms(<path>, format_in = "mzml"). I will add mzxml as an alias in the next release to make this more clear. Please let me know if for some reason RaMS can't read your files and we can try to figure out what the issue may be

[ethanbass]

I went ahead and added an "mzxml" alias into read_chroms, so you should be able to use `read_chroms(..., format_in="mzxml") in the latest version to read mzXML files with RaMS, as of (a50105e). Feel free to reopen if you run into any additional issues with this.
Ethan