No, I don't feel bad. I'm actually pleased that I've been able to
create it. And I'm sorry if I sounded aggressive.
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ProteoWizard seems to have poor documentation, because I don't see how
to do it.
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>fwiw, MzXML2Search does support mzML input files too.
So let me get this straight: The program is named MzXML2Search, and
when entering the command to see its usage, it says it expects
*.mzXML, and makes NO mention of mzML.can support mzML.
I think an update to its name and/or documentat
mzML is the new format that should be used, but I haven't seen any
programs out there that will convert mzML into mgf and ms2, like
MzXML2Search does with mzXML.
With some help from my professor, I've expanded ms-msrun to support
mzML and thus be able to convert mzML into mgf or ms2, but I'm
curio
> So how do you know if the protein is a decoy or not?
The entire database is reversed. They're all decoys. A search engine
is run on the original database and then run again on the reversed
database.
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As a note, Tide doesn't output pepXML, but I have created a converter
for it if anyone's interested:
http://github.com/JesseJ/pipeline/blob/master/pipeline0.01/src/tide_converter.rb
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If anyone's interested, I finally got msconvert to work, but it takes
extra effort to do when you have your pipeline running on a UNIX
machine.
I tried running msconvert under wine, but it or its dependencies kept
crashing, so we decided to set up msconvert on a Windows computer and
create a dedic
The decoy databases we use have no additional tags. It simply reverses
the sequences.
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Up till now I have just had ReAdW output mzXML, but when I tried to do
mzML, the program crashed. The program really doesn't say anything as
to why this happened, so I'm not sure what to do. Suggestions?
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The following text comes from the ReAdW READEME file:
Getting the code
The code for this program is released under the LGPL. It ca
Out of curiosity, what search engines did you have in mind?
On Jun 24, 9:41 am, Nathan Edwards wrote:
> The wiki says to send this request to the spctools-dev mailing list,
> but I can't find out where this list is, or how to send to it.
>
> I'd like to request the addition of a (few) search engi
I don't know, but if it's not a feature you can turn on or off, and
there's nothing wrong with the data, then your only choice might be to
go in and change the source code. I had a problem with X! Tandem
renaming output files by adding the date, and the only why I fixed
that was by changing the cod
I've tried getting this to work for a while now, but I keep getting an
error code of 256. I've tried different forms of the command, but this
is an example of one I've tried:
/usr/local/src/tpp-4.3.1/build/linux/xinteract -Ndata.pep.xml -iP
pipeline0.01/data/test-forward_tandem_1.pep.xml pipeline0
I'm trying to run a search on SpectraST, but the resulting pepXML file
has no search results. I must have done something wrong because other
search engines find hits just fine. Here's an example of what I'm
doing:
"build/linux/spectrast -cN test test.ms2"
"build/linux/spectrast -sD uni_human.fasta
You say that these duplicate peptides have the same score values, but
do they have the same protein ID/description?
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Um...that didn't help.
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For
I can't find any documentation on running Peptide or Protein Prophet.
Is there any out there?
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Also, I put down what I did on the Wiki in case anyone else needs to
do the same thing.
On May 14, 3:02 pm, Jesse J wrote:
> This question isn't critical, but I'm curious: why is it that the TPP
> comes with a version of X! Tandem that's about three years older than
> the
This question isn't critical, but I'm curious: why is it that the TPP
comes with a version of X! Tandem that's about three years older than
the current version?
On May 14, 2:53 pm, Jesse J wrote:
> Thanks, that worked out, both with installing TPP and fixing Tandem.
>
01865 2)87807 (CCMP - Mon-Thu)
> > Tel: (+44) (01865 2)75557 (Dunn - Friday )
>
> >
> > From: spctools-discuss@googlegroups.com [spctools-disc...@googlegroups.com]
> > On Behalf Of Jesse J [firstblackphan...@gmail.com]
> > Sen
I've been running some of the TPP tools under wine, but I'm trying now
to run them as Linux programs, or more specifically, Ubuntu 10.04. I
was following the instructions on the Wiki page for installing TPP
under Linux (http://tools.proteomecenter.org/wiki/index.php?
title=TPP_4.2.1:_Installing_on_
Is there a program that will convert a pepXML file to an mgf file?
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spctool
Oh, whoops, silly me. Since it said that it couldn't open the file, I
assumed it never created the pepXML file. Thank you for those points
though.
So then what is it upset about? Is it trying to open the mzXML file in
addition to the output xml file?
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I'm trying to run Tandem2XML to convert an X!Tandem output file to
pepXML, but I get an error every time I try to run it.
When I run: Tandem2XML /full/path/name/to/tandem_output.mzXML /full/
path/name/to/test.pepXML
I get the errors:
WARNING: Failed to open mzXML file.
Output will not con
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