Hello Matt,
We got it to work now, taking a detour but it works fine now. It was more a
problem reading the mzXML files and then ignoring certain things.
However, I have one more question: Where is in the latest format of mzXML
the isolation width of the precursor stored (set in the method of
No I don't think isolation width is representable in mzXML except perhaps with the pseudo-CV
mechanism which pwiz/msconvert doesn't support for mzXML. You probably want to switch to mzML. It
has a considerably richer metadata model, including isolation width.
-Matt
On 8/21/2012 11:15 AM,
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
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
Hello Kshitiz,
That I was asking in the post before. Due to a special method-setup in
XCalibur - I cannot use ReADW directly for conversion. We first have to
read out the raw-files with our own software and then need to save the data
again in a universal format, preferably mzXML format.
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
Hiya,
What about using ReAdW ? This is what we routinely use to convert RAW files
to mzXML.
Cheers,
Kshitiz
On Wednesday, August 8, 2012 4:40:47 PM UTC+1, wlstraube wrote:
Hello TPP-Team,
I would like to compile a mzXML file from a Thermo raw-file, which has an
internal structure that
