Re: [proteowizard-support] mzML: wrong precursor values

[Matthew C. <mat...@gm...>]

Hi Till,

What does the "Monoisotopic M/Z" field say in the scan header? That's what msconvert is using, 
unless it is outside the isolation window (which was an edge case we had to deal with for some 
firmware bug). If the firmware is giving the wrong m/z in this mass tag mode (which I'm not familiar 
with) and it's in the isolation window then there's not much we can do to fix that. You can try the 
recalculate precursor filter, and report the bug(?) to Thermo.

Hope this helps,
-Matt


On 10/30/2012 6:02 AM, Till Bald wrote:
> Hello,
> we usually convert all our RAW-files to mzML files through MSconvert
> (thank you for this great tool!).
> Our setup: Thermo LTQ Orbitrap, MS/MS experiments, MS2 scans are
> acquired in the Orbitrap.
> In addition, we measure in Mass Tag mode (searching for a mass tag of
> 12.07527 Dalton).
> Now we noticed that we get different values for the precursor mass:
> For example, the Thermo QualBrowser shows a precursor m/z of 659.12,
> while the mzML file has 654.423828125 (selected ion m/z). From our
> point of view, the QualBrowser shows the right value. Note that the
> right value also appears in the 'isolation window target m/z'.
> The wrong precursor m/z value appears only in the 'second' MS2 scan
> (peptide with mass tag), not in the 'first' MS2 scan (peptide without
> mass tag)
> I attached a screenshot for clarification.
>
> While measuring without the mass tag, all precursor masses in the mzML
> file are correct. So we assume that this is connected to the mass tag
> mode.
>
> Is this problem already known? Or do you have an idea how to solve
> this? We thought about using the 'isolation window target m/z' value,
> but this is not accurate enough.
> Thanks for your help.
> Kind regards,
> Till Bald
>
>
>
>
>
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