1. We routinely use msconvert on QExactive data, so I'd need to see your data file to understand why
it's not working.
2. Yes, it is frequently updated and bugs that are reported are usually fixed within a week. I'm
curious why you didn't set the method to collect multiple microscans per MS2 (which get combined
automatically) instead of collecting independent MS2s? We've pondered having this kind of capability
in msconvert for older Waters data where the microscans were not automatically combined.
-Matt
On 8/16/2012 6:44 AM, wlstraube wrote:
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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