There is an ExPASy tool to merge CID/HCD spectra from a Mascot MGF
format peaklist for this purpose. Can you go from RAW/MzXML/MzML into
MGF, use this tool, and then convert to dta for SEQUEST? We've done
iTRAQ on an XL, but only using PQD not mixed CID/HCD, so it's just a
suggestion to try, can't
Hi,
You don't need the mzXML file to be present to analyse the Mascot
results with the TPP tools. You will lose certain functionality
though, such as not being able to use the XPRESS / ASAPRatio
quantitation tools for SILAC data etc.
If you do have the mzXML files then the TPP tools work out
Just read this post and though I'd check our wine ReAdW output vs
native XP using diff. Like Jeffrey we're using Trapper and ReAdW on
Ubuntu (10.04 LTS), wine version 1.2. Were previously using it on
Ubuntu 9.04 for over a year, with whatever version of wine that had.
Never had any problems using
I expect you need to tweak the Apache config to tell it that it's OK
for the webserver to access that directory.
On Thu, Nov 4, 2010 at 7:59 AM, Cristian cristian.r...@gmail.com wrote:
Dear All,
We have problems seeing files in Petunia (Windows) under working data
directory of TPP installed
I may also add that if your data is in a location other than the Windows
default (C:\Inetpub\wwwroot\ISB\data\), you may need to make some tweaks to
Petunia, and possibly Apache. This post (and thread) has good information
on how to do it:
Brian is right. Try also looking in your log files to see what if any
errors are being reported. These are typically located in paths similar to:
C:\Program Files (x86)\Apache Software Foundation\Apache2.2\logs
C:\Program Files\Apache Software Foundation\Apache2.2\logs
On Fri, Nov 5, 2010 at
Hi Cristan,
You can check the post mentioned by Luis, infact it was mine :)
One correction, we also need tpp-bin folder along with wwwroot for data
directory to be other than C drive.
Thanks
On Fri, Nov 5, 2010 at 2:41 PM, Joe Slagel jsla...@systemsbiology.orgwrote:
Brian is right. Try
I just tried readw on wine for the very first time this afternoon
(version 1.2.1 on a RHEL 5.5 box); I'm impressed with how easy it was
to setup. Both very old LCQ and new Orbi RAW files generated mzXML's
that were *exactly* the same between wine and native Windows
conversions. 'diff' returned
I was having same problem with msconvert as described above (on
windows 7 64-bit). I installed MSfilereader and newest Proteowizard
package (to tpp-bin) as suggested. But now I receive a Caught
Unknown Exception error:
c:\Inetpub\tpp-bin\msconvert -v --mzML -o c:/Inetpub/wwwroot/ISB/data/
We have worked on merging PQD and CID spectra for iTRAQ before. Raw could be
converted to mgf using extract_msn.exe packed in Sequest/Bioworks. I can
provide a script to merge spectra with reporter peaks if you need. You may
find some description of the method in JPR.7:4831.
Now I have also
Hi Todd,
This is most likely due to the Petunia's obsolete way to specify the
centroiding option to msconvert. It should run just fine if you leave that
off; I can send you a patch offline so that it works, or wait for our next
release.
Cheers,
--Luis
On Fri, Nov 5, 2010 at 6:40 PM, tgreco
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