#5 msconvert gets m/z values wrong

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nobody
None
5
2012-12-28
2011-10-27
Daniel
No

I am trying to use msconvert for conversion of Waters RAW files to the mzXML format, but I get wrong m/z values in my mzXML files (see screen shot attached). The basepeak m/z is however correctly recognized (see bottom table in the screen shot).

Command used for conversion:
msconvert.exe --mzXML -v --filter "scanEvent [1,1]" DW522.raw

ProteoWizard release 2.2.3073
MassLynx V4.1
On WindowsXP SP3

Discussion

  • Daniel
    Daniel
    2011-10-27

    Mass spectrum with wrong m/z assignments

     
    Attachments
  • Mark Philo
    Mark Philo
    2011-11-17

    Hi Daniel,
    I am getting the same issue. I am running the Synapt G2 with Leu Enk lock mass.

    If I take a spectrum in MassLynx, I will obtain an accurate mass. If I export to ASCII or CDF using DataBridge, I get the same accurate mass.
    Only when I use "msconvert" to mzxml so I get a wrong masses, something like 0.2 Da.

    Is it perhaps something to with the lock mass correction?

    -- Mark --

     
  • Daniel
    Daniel
    2011-11-18

    Hi Mark,

    my data also come from a Synapt G2. I switched to DataBridge CDF export
    which work s fine.

    I don't think it is a lock mass issue, because in the msconvert results
    the base peak is reported correctly. (In the separate base peak field,
    but not in the whole scan data.)
    So maybe it is an encoding problem?

    - Daniel