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Description:
Open forum for discussing Seattle Proteome Center proteomics tools, asking questions, and suggesting new features.
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Setting up TPP - unable to access /tpp/html files?
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Hi Everyone,
I started setting up the TPP on Ubuntu 9.04 / Apache2 over the weekend
following the instructions found at
[link],
and have had a few minor issues (so far). The setup seems to have gone
fine, and I can log into /tpp/cgi-bin/tpp_gui.pl and all that jazz.... more »
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Export result data for blast?
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Hi guys, I'm running a couple of searches with an un-annotated
datbase.
As such I would like to take the results from the prot.xml file and
run a blastP search with the sequences against an annotated related
databases.
Is there any easy way to export fasta sequences of a search together
with their protein ID? I've only come up with a very roundabout way... more »
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patch: Sqt2XML fixes
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It doesn't look like this patch ever made it into the SVN tree. Could
someone look at adding it? I think someone here's going to mention
this program in a paper, but without this patch this program doesn't
function correctly. Thanks!
[link]... more »
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OMSSA files with PeptideProphet
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Hello everyone,
I have .omx result files (from OMSSA browser 2.1.1) and I would like
to use the PeptideProphet (TPP v4.3.1).
However, the PeptideProphet only accepts .pepxml files, how could I do
to run this process from my OMSSA result files?
I have seen that a converter tool exist (omssa2pepxml) but I do not... more »
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MzXML2Search problem (Agilent msconvert-ed data)
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MzXML2Search conversion to mgf fails for me on mzXML / mzML created
using msconvert from Agilent 6520 QTOF data.
Trapper numbers spectra using an index starting at 1, whilst msconvert
uses the Agilent scan ID (can be a very large number). MzXML2Search
conversion of the resulting file into mgf then fails once it reaches a... more »
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ReadW and Orbitrap Exactive output files
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Hi,
This week I converted a number of Orbitrap Exactive files
using the installed Xcalibur (Thermo Exactive 1.1) and the current
ReadW (4.3.1).
The resulting *.mzXML files had the msLevel="0", polarity="any". Also
raw files contain scans from four different functions ESI+ full lock,
ESI+ full MZ, ESI- full lock and ESI- full MZ. All scans from these... more »
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PHP - Apache
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Hi,
I have using ubuntu 9.04 linux, Yesterday I installed PHP and Apache.
Both are working fine, can able to execute those commands.
But today after starting apache, I used start execute my php files but
I'm getting the below error.
If I try with [link], some error displayed.
Forbidden... more »
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Mayu parsing TPP output
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Hi,
I was hoping someone might know why my Mayu software won't work. I
have been using Mayu on .pep.xml output from TPP with a fasta file
that includes Decoy sequences.
The Mayu software appears to successfully read the fasta file.
However, I believe it can't parse the pepxml output properly (even... more »
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"base_name" constraint in pepXML
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Hi!
I'm working on the pepXML parser in OpenMS. I've been confronted with
a type of pepXML file I hadn't seen before, where search results from
different search engines - but for the same experiment - were
collected in one file (with one "msms_run_summary" per search engine).
I've added (maybe prematurely) support for this to the OpenMS parser,... more »
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using system libs for extern deps on linux build
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Hi all,
I am trying to get together a chef "cookbook" for downloading and
building the TPP on a linux system. (Chef is an open source systems
administration, bootstrapping and configuration system from
opscode.com).
I would be nice to separate out some of the pieces into their own
"recipes", especially the external dependencies such as boost and... more »
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