Re: [proteowizard-support] Issue with Waters MSe conversion

[Jan S. <sta...@gm...>]

The precursor m/z is the midpoint between the min and max in the recorded
mass range as far as I remember. So the idea is a precursor +/- half the
width of the mass range.

On Tue, Jul 11, 2023 at 6:19 PM Chambers, Matthew <mat...@gm...>
wrote:

> When you see a spiky TIC like that it's indeed usually because there's two
> or more different functions/scan events interleaved. For MSe that's
> certainly the low energy and high energy functions (the latter being
> considered as "MS2" but only out of convention since it doesn't have a real
> precursor).
>
> On 7/11/2023 12:08 PM, Brian Pratt wrote:
>
> I’d recommend eyeballing the mzXML - you’ll find that it’s all MS1, I
> think. How mzmine deals with displaying that, I don’t know.
>
> On Jul 11, 2023, at 8:05 AM, Taylor, MJC, Mnr [mt...@su...]
> <mt...@su...> <mt...@su...> wrote:
>
> 
>
> Thanks.  So the chromatogram is then a blend of MS1 data at the top of the
> peaks and MS2 data at the bottom of the peaks?
>
>
>
>
>
>
> *From:* Brian Pratt bs...@pr...
> *Sent:* Tuesday, July 11, 2023 5:02 PM
> *To:* Taylor, MJC, Mnr [mt...@su...] <mt...@su...>
> <mt...@su...>
> *Cc:* su...@pr...
> *Subject:* Re: [proteowizard-support] Issue with Waters MSe conversion
>
>
>
> CAUTION: This email originated from outside the Stellenbosch University
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>
> That’s correct. Note that the window is extremely wide - it’s an all ions
> fragmentation. There’s no single precursor per se, but mzXML expects some
> value there.
>
> Sent from my phone, with apologies for brevity and strange autocorrections
>
>
>
> On Jul 11, 2023, at 6:05 AM, Taylor, MJC, Mnr [mtaylor--- via
> proteowizard-support <pro...@li...> wrote:
>
> 
>
> Good afternoon,
>
>
>
> I am having some issues converting my Waters MSe data to mzXML. As can be
> seen in the screenshot below, the Precursor ion for all scans is 770.  The
> raw data from a Waters G2 qTOF was converted using MSConvert
> 3.0.23191-2fd18c2 using 64-bit precision with Peak Picking as the only
> subset.
>
>
>
> Please can you comment.
>
>
>
> Thanks
>
>
>
> Malcolm Taylor
>
> University of Stellenbosch
>
>
>
> <image001.png>
>
>
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