Hi Brian,
Thanks for your reply. I also figured out the variant of the title
string. I think this depends on the file type searched (mgf or mzdata)
and the version of Mascot as well. Thanks for having fixed that.
I am no informatician and I am not sure I understand how I should
proceed to get
I haven't tried your suggestion of running it on another distro yet
Natalie, but I did get the latest version when that was announced and
I got a little bit further. I was able to run 'make all' without any
errors, but when I run try to run 'make install' I'm back with the
error message
dear list,
when running following command (tpp 4.3.1)
/usr/local/apps/tpp/bin/xinteract
-N/IMSB/results/workflow/45/Xinteract_/Xinteract.pep.xml -dDECOY_ -OAlIwp
/IMSB/results/workflow/45/Tandem2PepXML_/O08-10105_c.mzXML.pep.xml
i get following error:
(FWIW, Ubuntu is a flavor of Debian)
That's interesting - does make clean all work after your first make
all? It sounds like the build is somehow changing the environment, or
maybe even its own makefiles...
On Thu, Sep 17, 2009 at 11:45 PM, Eliza blond...@googlemail.com wrote:
I haven't
My guess is its nothing you're doing wrong - iProphet is still pretty new
and it's probably confusing the PepXMLViewer parser. If you can upload the
file that crashed pepXMLViewer to ftp://insilicos.serveftp.net/pub I Natalie
or I will be happy to have a look.
Brian
On Fri, Sep 18, 2009 at 6:47
Dear friends,
I have a large protein database (2G) in fasta format. I want to use it
as decoy database during protein identification and append it to a
target database. So I need to modify the ID name in this fasta file.
How should I do it quickly in batch? Is there any software that can
satisfy
Have a look at the decoyfasta tool that ships with TPP.
On Fri, Sep 18, 2009 at 10:21 AM, rhodea rho...@gmail.com wrote:
Dear friends,
I have a large protein database (2G) in fasta format. I want to use it
as decoy database during protein identification and append it to a
target database.
hi brian,
many thanks for looking into it!
i also tried to process the file with different options but always the same
error.
it would be awesome if you (or natalie) could test the uploaded files
(andreasquandt_090918.zip) as i otherwise do not know how to solve this
problem :-(.
cheers,
andreas
Does anybody know what this means? How does it affect the data and/or
metadata?
Thanks,
Matt
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If you mean enhanced scan speed and you're using an ion trap (linear or
LCQ), I'd highly recommend choosing it. The scan speed is slightly slower
than the normal speed and allows for better mass accuracy and a better
chance at seeing the charge envelop (thus better able to determine charge
Hi Jane,
Thanks for answering so quickly. This filter line was found on an LTQ XL
RAW file. Does the enhanced scan speed you mention result in the 'E'
in the filter line?
Thanks,
-Matt
Science Gurl wrote:
If you mean enhanced scan speed and you're using an ion trap (linear
or LCQ), I'd
Yes, you'll see something like: *ITMS + p NSI E full scan (400-1800)* in the
scan filter/header information on the file.
Does this help?
-jane
On Fri, Sep 18, 2009 at 4:30 PM, Matthew Chambers
matthew.chamb...@vanderbilt.edu wrote:
Hi Jane,
Thanks for answering so quickly. This filter
That hits the nail on the head. When I encounter these scans, I will add
this term to the metadata:
[Term]
id: MS:1000497
name: zoom scan
def: Special scan mode, where data with improved resoltuion is acquired. This
is typically achieved by scanning a more narrow m/z window or scanning with a
Hi Andreas,
I think you are doing everything correctly. The soruce of the problem is here:
PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 200909181208 (linux))
akel...@isb
read in 0 1+, 1135 2+, 137 3+, 18 4+, 0 5+, 0 6+, and 0 7+ spectra.
Initialising statistical models ...
Iterations:
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