MzML compatibility with Proteome Discoverer

[caetera]

Hello,

mzML files produced by Monocle cannot be processed with Proteome Discoverer (tested with version 2.5). The apparent reason is unsupported cvTerms used for selectedIon.
Please, consider using MS:1000041 (charge state) and MS:1000744 (selected ion m/z) instead of MS:1000633 (possible charge state) and MS:1000827 (isolation window target). After the change (see the script below), the file can be processed. As a side note it might also improve the compatibility with other tools.

from lxml import etree

def heal_selected_ion(filepath):
    m = etree.parse(filepath)
    
    ns = m.getroot().nsmap
    ns['a'] = ns[None]
    
    for sel_ion in m.findall('//a:selectedIon', namespaces=ns):
        for el in sel_ion.getchildren():
            if el.get('accession') == 'MS:1000633':
                el.set('accession', 'MS:1000041')
                el.set('name', 'charge state')
            elif el.get('accession') == 'MS:1000827':
                el.set('accession', 'MS:1000744')
                el.set('name', 'selected ion m/z')
    
    m.write(filepath, xml_declaration = True, pretty_print = True, encoding = 'UTF-8')