Hi Julia,
Try this post for .msf converter.
Proteome Discoverer's .msf to TPP input files (pepXML)
http://groups.google.com/group/spctools-discuss/browse_thread/thread/bbfad1a9a04d775f/9497da1edc9fd2d0?lnk=gst&q=Proteome+Discoverer%27s+.msf+to+TPP+input+files+(pepXML)#9497da1edc9fd2d0.
I have had
Actually if you follow this thread it looks like some progress has
been made.
http://groups.google.com/group/spctools-discuss/browse_thread/thread/bbfad1a9a04d775f/9497da1edc9fd2d0?lnk=gst&q=Proteome+Discoverer%27s+.msf+to+TPP+input+files+(pepXML)#9497da1edc9fd2d0
On Dec 24, 3:48 pm, WoA wrote
Hi,
I do not think the pep.xml from PD is useable by TPP. Scaffold can
use PD .msf format and I know some others expressed interest in
converters for the various PD outputs but never saw any movement
forward for the PD xml format. A search of this group will come up w/
many related threads.
On D
Done grabbed latest off site and mgf works.
On Jul 27, 5:57 pm, Matthew Chambers
wrote:
> I highly recommend a newer version of pwiz!
>
> -Matt
>
> On 7/27/2011 4:30 PM, DD wrote:
>
>
>
>
>
>
>
> > We have 2.0.7 file formats and the cmd line for msconve
We have 2.0.7 file formats and the cmd line for msconvert works for
mzXML and mzML. It fails on .mgf conversion. We also run MzCv which
is a GUI for msconvert and it only works for mzML. The GUI still
points to same cmd line msconvert so not sure why it fails but it is
the same unable to open fi
I know Massmatrix (free/open-source) accepts ETD, ECD and CID/ETD. It
is easy to install. It is a nice piece of software.
DD
On Jul 25, 5:45 am, Amit Kumar Yadav
wrote:
> Dear All,
>
> I want to know about some ETD search tools, preferably free/open-source.
>
> I tried Mascot,
I think for much of what you are trying to do (access control,
uploading data, cluster work and maybe as a benefit to end user as
well) you might want to look at Labkey Server which supports TPP
(v4.3 i think).
On May 6, 8:15 am, Bjorn wrote:
> Hi David,
>
> About the threads: if you decide to us
to feed ProteinProphet. PepProphet can
feed both. All of these tools can be used to combine pep.xml files.
So for me PepPro feeds IPro which then feeds ProPro
Hope it helps and please anyone correct me where I am wrong.
DD
On Mar 4, 12:22 am, Simon Michnowicz
wrote:
> Dear Group,
> I hav
Yes. If you click on protein in pep.xml viewer you should see your
highlighted seq. (reading from N to C)
On Mar 5, 3:00 pm, Olesya wrote:
> Good afternoon everyone,
> I have a bit of a rookie question: Does Peptide Prophet (pep.shtml
> files) list peptide sequences from N-terminus to C-terminus
arch, and thus we can
> make comparison with other search results which are measured by
> peptide
> prophet.
>
> On Mar 4, 5:39 pm, DD wrote:
>
> > No params file it is set in either workflow or standalone sequest
> > que. They are dropdowns to choose pre-populated mo
I can drop off examples of export options if someone else want s to
have a look see. I will also discuss w/ Thermo to see if there is
something they can do on their end quickly.
On Mar 4, 7:08 pm, Jimmy Eng wrote:
> You should search your Proteome Discoverer box for a file named
> 'sequest.param
into
peptide prophet?
DD
On Mar 4, 7:08 pm, Jimmy Eng wrote:
> You should search your Proteome Discoverer box for a file named
> 'sequest.params' as I don't have access to the Thermo version. In
> fact, I wouldn't even know if sequest.params still exists under
CX.doc, but the
> file has only 143 pages (I have XCalibur 1.4).
>
> Matthias
>
> On Apr 20, 5:51 pm, DD wrote:
>
>
>
> > b)C:\Xcalibur\system\programs\XRawfile OCX.doc p. 153-156 is what you
> > want if you are going to go the activeX route. Looks like pwiz ha
this could be OOD.
Later in the week I should be able to pull out our deprecated
functions for you to use for this functionality.
DD
On Apr 20, 3:20 am, brennmat wrote:
> Thanks for this suggestion. I tried rawfile.exe from the XDK examples.
> It does export the data from the ECD, but the
Maybe give XChroDisplay in XDK. You could also call rawfile.exe in
XDK which allows exporting of analog data. We did do this at one time
(for LC data) so will ask group how. We stopped when we started using
Promass (again for LC data) which also pulls this data.
On Apr 16, 11:49 am, brennmat
Hi,
Any idea if converters from mzXML and/or other open formats to
manufacturers binary format (.d for example)exist?
DD
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