So perhaps it is something wrong with my system? I just placed the
pep.xml file that Jimmy created for me into my c:/Inetpub/wwwroot/ISB/
data folder.
Via petunia I tried to run PeptideProphet with that file, I get the
following error:
Output Files
* c:/Inetpub/wwwroot/ISB/data/interact.pep.
I'm stumped as I can't replicate the error. Ruby sent me her data and
I had no problems running Out2XML to generate the pep.xml file. Both
on a Windows box and under Linux.
- Jimmy
On Mar 1, 1:58 pm, Ruby wrote:
> Hi-
> I just downloaded the latest version of TPP this week, so version:
> TPP v
Hi,
Although Thermo people told me otherwise Xcalibur works fine under win
7-64 bit. so I managed to convert the.raw files to mzxml format and I
tried to run a sequest search using the params file from bioworks that
I dont have any access right now. TPP(4.4) is looking for sequest
under bioworks fo
Thank you for the reply, I sent them the same question.
gogce crynen
On Mar 3, 1:12 pm, Joe Slagel wrote:
> Gogce,
>
> It sounds like this might be a problem with msconvert itself. Can you cross
> post your question to their mailing list? Its at supp...@proteowizard.org.
>
> -joe
>
>
>
>
>
>
>
Hi all:
May I check with one question about checking ASAp ratio? The data was produced
with velo mass spectrometry and totally have 40 fractions. After using TPP
analyzed the data, I clicked the ASAP ratio and want to see the details of each
peptide ASAP ratio or Xpress ratio. I do not know what
Gogce,
It sounds like this might be a problem with msconvert itself. Can you cross
post your question to their mailing list? Its at supp...@proteowizard.org.
-joe
On Thu, Mar 3, 2011 at 6:57 AM, gkayihan wrote:
> I tried to post my question in this thread
>
> http://groups.google.com/group/
Yes, I can see why mzXML with interlaced m/z and intensity would get much worse compression here.
There is pretty steady baseline on the data and since it's profile there are tens of thousands of
data points per spectrum. It's much better to compress the intensity and m/z arrays separately in
th
Thanks for the reply. Can't seem to upload to the group's list, so
here is a link
http://dl.dropbox.com/u/11659021/subset.7z
Has two files generated below. If you want, I can include any files
upstream of this conversion too if that would help.
- Ben
On Mar 3, 11:33 am, Matthew Chambers
wrote:
>
If you want to post some samples to the list, use msconvert with an index
filter. Try:
msconvert original.mzML -o subset --filter "index 0-100" -z
msconvert original.mzML -o subset --filter "index 0-100" -z --mzXML
And attach both the subset mzML and mzXML for comparison.
Thanks,
-Matt
On 3/3/
I haven't played around with compression, but that would be simply
adding a -z [ --zlib ] correct? I am using this page more so than
the help on sourceforge for command arguments.
http://groups.google.com/group/xcms/msg/53e2a2b462a5448c
Thanks for the help, and I will let you know if something b
I tried to post my question in this thread
http://groups.google.com/group/spctools-discuss/browse_thread/thread/e480de4eaa396eac/2df8eef8bd7d29af?lnk=gst&q=msfilereader#2df8eef8bd7d29af
but it never posted on the website to I am trying it again as a
separate thread.
I am running tpp 4.4 on windows
A well constructed mzXML file would normally be somewhat smaller than
its mzML equivalent - make sure you've got peaklist compression turned
on (IIRC the msconvert default is no compression, which seems like a
Bad Thing to me but there you have it).
On Wed, Mar 2, 2011 at 10:37 PM, ben wrote:
> I
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