Dear All,
We have a similar problem in that we don't see any retention times (they
are all zero) from the X!Tandem+Tandem2XML-generated pepXML files. This
problem appeared with the 4.6 version of the TPP with the updated X!Tandem,
previously we had no problems with it. For SpectraST we still
Hello TPP-Team,
I would like to compile a mzXML file from a Thermo raw-file, which has an
internal structure that cannot be converted by msconvert.
I am able to read out the raw-file and process it, but now want to save it
as a mzXML.
Therefore, without reinventing the wheel, I would like to
Hello. I came across this post while doing a google search for conversion
of msf files to pepXML. I am trying to use Proteome Discoverer output with
a protein assembly tool called IDpicker, but of course it is impossible
to export pepXML format from Proteome Discoverer. Has there been a
The best thing would be to just use your new reader code to extend
msconvert so that it *does* read your file. Then you can output to
anything msconvert already handles.
- Brian Pratt
On Wed, Aug 8, 2012 at 8:40 AM, wlstraube stra...@imp.ac.at wrote:
Hello TPP-Team,
I would like to compile a
Dear Brian,
Thank you very much for the quick response.
If I get you right, I should take the msconvert source code and implement
our code. This sounds logically, but for a first try I would try to keep it
simple.
I would need only the part which writes down the required parameters. Would
For simplicity, you would probably want to go with the hacking up the
old readw code. But if you have any plans for sharing your work or
using it very far into the future then you're better off with
ProteoWizard and msconvert since that gets maintained and offers more
output formats.
Brian
On
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
Can you post what your RC number is? My test box over here using 4.6 RC9
rev 0 correctly displays the retention times with PepXML Viewer under the
retention_time_sec column.
Thanks,
Mike
On Wednesday, August 8, 2012 6:42:05 AM UTC-7, magnus@gmail.com wrote:
Dear All,
We have a similar
