Hi,
I am a first time user of XCMS Online and am having some difficulties. I have uploaded 2 data sets of converted (to mzXML) thermo exactive data.
I've tried 2 parameter settings - HPLC-Orbitrap and HPLC Single Quad. On both occassions I have recieved the error - "No MS1 data?"
Is it my parameter setting that is causing this problem, what setting should be used for Exactive data? I have had no problems on other software packages with these mzXML files.
Thanks.
Hi,
what kind of MS experiments is that ? MRM like ? Or really plain MS1 full scans ?
Can you check the mzXML file, and find those <spectrum ...> lines,
and see whether it says something about ms level ? In doubt just post
the area at the <spectrum>.
Steffen
The obsolete ReAdW converter assigns MS scans as msLevel=0 for some reason (msLevel=0 is invalid, it should be msLevel=1).
Some programs work around this problem by assuming msLevel=1 in that case. XCMS doesn't make this assumption, therefore the error message.
I would recommend converting the files with proteoWizard's (http://https://xcmsonline.scripps.edu/docs/fileformats.html) converter instead.
Thanks for the advice,
I will convert my raw files using Pwiz and try again.
The Exactive produces high res full scan data files (not MRM or MS/MS).
In the meantime I'm trying XCMS online again using Agilent QTof data so we'll see how that goes!
Mike.