Dear All,
I look for an opportunity assign MS3 spectra as MS2.
Until now in the common converters I could not find such option.
I thought that in the past it was from time to time usually done to
merge MS2 and MS3. Even this option I could not find specifically in
MSconvert.
Could you please give me a hint if there is such option that I could
routinely convert *.raw files from LTQ-Orbitrap acquistion files to
mzXML and merge MS3 into MS2.
Thanks
Dominik
On 8/20/2012 10:42 PM, Matthew Chambers wrote:
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
--
Dr. Dominik Schwudke
Group Leader
National Centre for Biological Sciences
Tata Institute of Fundamental Research
GKVK, Bellary Road,
Bangalore 560065, India
Phone +91-80 – 2366 6499
+91-80 - 6717 6499
[email protected]
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