Just an FYI, I took a quick look at the difference between msconvert in TPP
4.5.2 and 4.6.2 and it looks as if the version in 4.5.2 doesn't support the
sortByScanTime filter.  I'm going to assume that this is a relatively new
filter added by the ProteoWizard folks.

Any chance you can provide the mzML files created using msconvert from
4.5.2 and 4.6.2 so that we can take a look to see what may be wrong?

-Joe



On Mon, Apr 29, 2013 at 3:46 PM, ChargedPeptide <[email protected]> wrote:

> Okay, I realized that MSConvert from TPP 4.5.2 just ignored
> my  sortByScanTime filter for msconvert, tried this with 4.6.2 and it
> works. So it seems I might have to give up my sorted scans. Sniff.
>
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