Hello Matt,
There are actually more issues with msconvert.
(1) I have difficulties that msconvert correctly converts standard
thermo-raw-file of QExactive runs. There seems to be that
- scan data is corrupt (likely encoding problems)
- Thermo filterline is missing (as specified by mzXML)
I have to admit that I used the graphical user interface
(MSConvertGUI.exe), thus I am not sure, if this causes the problem.
(2) For the special raw-file format we obtain (and the reason I started the
post), it is just about having several MS2 scans of the same precursor and
then merging the MS2 spectra together.
Question: is the msconvert tool (what I think is a fantastic thing to have)
currently maintained by someone and updated with latest formats ?
Best,
Werner
On Thursday, August 9, 2012 6:51:17 PM UTC+2, matt.chambers wrote:
>
> Hi Werner,
>
> Assuming you eventually want to publish your method and have other people
> adopt it, the best thing
> to do would be to make msconvert handle your RAW files. Having other users
> of your method be able to
> use a widely adopted converter is better than creating a new ad-hoc
> solution.
>
> I'm curious what you did in Xcalibur to make your files incompatible with
> msconvert. Can you share a
> small example RAW file?
>
> Thanks,
> -Matt
>
>
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