Hi, I've been using both trapper and msconvert to convert Agilent MassHunter ".d" data to mzXML. I'm using msconvert from the proteowizard 1.6.0 distribution, and I'm using the standalone trapper 4.3.1 from sashimi.
I've noticed that the msconvert output is structured differently from the trapper output, and appears to break at least two rules specified in the mzXML 2.1 tutorial (http://sashimi.sourceforge.net/ schema_revision/mzXML_2.1/Doc/mzXML_2.1_tutorial.pdf). (1) Scan numbers (as per the scan/@num attribute) are supposed to start from 1, and ascend sequentially (presumably without skipping). The msconvert output numbering appears to be arbitrary (for me, it starts at 2273 and ascends with gaps). (2) Scan elements representing MS2 scans are supposed to be nested within the elements representing their precursor MS1 scans. The msconvert output does not perform this nesting. The trapper output appears compliant. Are these differences causes for concern? Is it possible that SPC tools (or others) might function incorrectly when processing msconvert- generated mzXML files? Thanks, bio.x2y -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
