OMSSA files with PeptideProphet

[Loïc JOFFRE]

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
understand how to use it, I have just found the source code of this
program on the web.

I am working on Windows XP.

Thanks a lot,

Loïc Joffre

[Brian Pratt]

I don't personally know anything about it, but a quick googling brings up this thread that may help you find someone who does:

http://groups.google.com/group/spctools-discuss/tree/browse_frm/month/2007-11/53e4277da13cd30b?rnum=91&_done=%2Fgroup%2Fspctools-discuss%2Fbrowse_frm%2Fmonth%2F2007-11%3F

- Brian Pratt

[Loïc JOFFRE]

Thank you Brian, but I have already seen those posts, and they only
explain that issues exist but not how to do.
If anyone knows?

Thanks a lot,
Loïc

On 17 nov, 17:04, Brian Pratt <brian.pr...@insilicos.com> wrote:
> I don't personally know anything about it, but a quick googling brings up

> this thread that may help you find someone who does:http://groups.google.com/group/spctools-discuss/tree/browse_frm/month...

[Loïc JOFFRE]

Thank you Brian, but I have already seen those post and they only
explain taht issues exist but no how to do.

If anyone knows?

Thanks a lot,
Loïc

On 17 nov, 17:04, Brian Pratt <brian.pr...@insilicos.com> wrote:

> I don't personally know anything about it, but a quick googling brings up

> this thread that may help you find someone who does:http://groups.google.com/group/spctools-discuss/tree/browse_frm/month...

[David Shteynberg]

Hello,

There is an option to output pepXML directly from OMSSA. Also OMSSA
provides a pepXML converter. When you run the TPP on OMSSA results
you have to specify the special option -P to InteractParser to fix the
protein names in the OMSSA output, also the enzyme option should be
given at the InteractParser step. To analyze OMSSA results with the
TPP the current model requires the use of the non-parametric model,
which requires Decoy in the database. Since OMSSA maybe biased in the
order in which it reports equivalent hits, it is also recommended that
you randomly order the sequences in your fasta database.

Hope this helps,
-David

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[Vensel, William]

Hi David,

Could you please point to a tool that will allow randomization of the sequences in a fasta dayabase.

Thanks,

Bill

[David Shteynberg]

Hi Bill,

Attached is a script and library dependency that will take two fasta
files and randomly interweave their entries. The idea is that one
file is your forward sequences the other is the reverse sequences, the
output goes directly to the console so you would have to redirect it
two a file. You have to use the commandline to use these tools. Copy
both files to one directory, and put your fasta files in the same
directory then open a commandline and switch to the this directory,
then you should be able to run this command:

perl mergeFasta.pl forward_DB.fasta decoy_DB.fasta > merged_DB.fasta

-David

[Vensel, William]

David,
Thanks

[Loïc JOFFRE]

Hello David,

I was looking everywhere on my OMSSA browser and in the OMSSA on line
and I really do not see any option to output pepxml or any pepxml
converter...
Are you considering that .omx files are pepxml files?
Because I could not use its on TPP...
Could you give me the steps to output pepxml on OMSSA?

Thanks in advance,
best regards,

Loïc

On Nov 23, 9:17 pm, "Vensel, William" <William.Ven...@ARS.USDA.GOV>
wrote:

> >> For more options, visit this group athttp://groups.google.com/group/spctools-discuss?hl=.

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> - Show quoted text -

[Matt Chambers]

It's not in the online command-line manual, but it's in the usage
statement for omssacl:
G:\work\omssa\omssa-2.1.7.win32>omssacl
USAGE
omssacl.exe [-h] [-help] [-xmlhelp] [-pm param] [-d blastdb] [-umm]
[-f infile] [-fx xmlinfile] [-fb dtainfile] [-fp pklinfile]
[-fm pklinfile] [-foms omsinfile] [-fomx omxinfile] [-fbz2 bz2infile]
[-fxml omxinfile] [-o textasnoutfile] [-ob binaryasnoutfile]
[-ox xmloutfile] [-obz2 bz2outfile] [-op pepxmloutfile] [-oc
csvfile] [-w]
[-to pretol] [-te protol] [-tom promass] [-tem premass] [-tez prozdep]
[-ta autotol] [-tex exact] [-i ions] [-cl cutlo] [-ch cuthi] [-ci
cutinc]
[-cp precursorcull] [-v cleave] [-x taxid] [-w1 window1] [-w2 window2]
[-h1 hit1] [-h2 hit2] [-hl hitlist] [-ht tophitnum] [-hm minhit]
[-hs minspectra] [-he evalcut] [-mf fixedmod] [-mv variablemod] [-mnm]
[-mm maxmod] [-e enzyme] [-zh maxcharge] [-zl mincharge]
[-zoh maxprodcharge] [-zt chargethresh] [-z1 plusone] [-zc calcplusone]
[-zcc calccharge] [-pc pseudocount] [-sb1 searchb1] [-sct searchcterm]
[-sp productnum] [-scorr corrscore] [-scorp corrprob] [-no minno]
[-nox maxno] [-is subsetthresh] [-ir replacethresh] [-ii
iterativethresh]
[-p prolineruleions] [-il] [-el] [-ml] [-mx modinputfile]
[-mux usermodinputfile] [-nt numthreads] [-ni] [-ns] [-os] [-nrs]
[-logfile File_Name] [-conffile File_Name] [-version] [-version-full]
[-dryrun]

-op is the option you're looking for.

-Matt

Lo�c JOFFRE wrote:
> Hello David,
>
> I was looking everywhere on my OMSSA browser and in the OMSSA on line
> and I really do not see any option to output pepxml or any pepxml
> converter...
> Are you considering that .omx files are pepxml files?
> Because I could not use its on TPP...
> Could you give me the steps to output pepxml on OMSSA?
>
> Thanks in advance,
> best regards,
>

> Lo�c
>

[David Shteynberg]

I believe its only commandline enabled. This is something to ask the
OMSSA developers.

-David

> For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
>
>
>

[Loïc JOFFRE]

I do not have any omssacl.exe file. I am using the OMSSA Browser and
to use it, I only have an "OMS_Browser" on which I double click to
launch the Omssa browser.
Where this executable can be downloaded?
Thanks,

Loïc

On Nov 24, 2:51 pm, Matt Chambers <matthew.chamb...@vanderbilt.edu>
wrote:

> > Lo c- Hide quoted text -