Error message when opening Waters DDA .mzML file

[Gscorreia89]

Hi,

I am experience the following warnings + error message when trying to process a Waters DDA mzML file with
pa <- purityA(mzMLFile)
MS2 data has no associated scan data, will use most recent full scan for information, followed by
Error in assessPuritySingle(filepth = pa@fileList[[i]], mostIntense = mostIntense, : task 1 failed - "argument is of length zero"

This file was converted using msconvert and the Waters DDA processing option, and can be downloaded in this link:
https://drive.google.com/file/d/1QPIyTA5fXbBl5YnhoD1QFk6mKOtjRpD7/view?usp=sharing

I came accross this previous issue - Processing Agilent QToF files and I believe the root cause to be the same. The files converted in this manner are missing the "isolation window lower offset" and "isolation window upper offset" in the <isolationWindow>, and "patching" the mzML file to include these with a fixed dummy value of 1 fixed the problem.

Would it be possible to add a check and more explicit error message for this case? And does it still make sense to use purityX measures if this value is not present? I will raise an issue with msconvert as well to see if they can standardise the mzML conversion to include this.

Thanks,
Gonçalo