Does Peptideprophet accept only a limited no. of pepXML files?

[Bernt]

Dear all,

I wonder if anyone has encountered this problem: For < 80 files,
Peptideprophet works normally, but when there are more than 80 files,
it doesn't start at all.

If we split them up into 2 batches to run peptideprophet, the
statistical distributions that we obtain would be different since it
may happen that we unknowingly choose a group of poor scoring spectra
to model for 1 batch, while the other batch contains high scoring
ones. Would the peptideprophet probabilities obtained for the poor
scoring batch be reliable ? Ideally we should analyse the distribution
across all the files from a single sample (separated into different
protein fractions) altogether, isn't it?

Would really appreciate if someone could enlighten on this, and
whether this can be gotten around by simply merging the some of the
smaller pepxml files in the first place.


Thanks,
Bernt

[Brian Pratt]

What operating system are you on (windows, linux etc)? My guess is that
it's probably about the length of the command line, rather than the file
count. We've had issues with this in the past, it might be borken again.

Brian

[Bernt]

Hi Brian,

Thanks for your response. I'm using TPPv4.2 Rev 1 on Windows XP. I
read the thread on "limit on number of pep.xml files that can be
analysed with interact" before, and Eric Deutsch was suggesting using
<xinteract *.pep.xml> on the command line. I tried it, and it started
processing all the 100 over files i had, but in the end there was a
problem with the generated interact.pep.xml file. Were you going to
suggest this <xinteract *.pep.xml> method?


Bernt

[Brian Pratt]

That's the issue I was thinking about, yes - so it sounds like using the
"xinteract *.pep.xm" approach you're on to a new and different problem,
then?

[David Shteynberg]

What was the problem with the final generated interact.pep.xml file?
Can you verify that all of your pep.xml files are complete? Check
their size and starting and ending tags for completeness. If there
are any error message please post them here.

-David

[Bernt]

Hi David,

Thanks for your response, I realised the xinteract has to be used with
*.pep.xml behind the options. Previously I used it before the options.
It manages to generate a working interact.pep.xml with all the
PeptideProphet probabilities. But the .shtml file showed an error:

http://localhost/ISB/data/OC/OGEmRPTD10/OGEmRPTD10_Tandem_interact.pep.shtml
[an error occurred while processing this directive]

This is not a big problem for me. I can live with it. The problem that
remains is the ion spectra could not be viewed in the PepXML browser.
I have put it in a separate post, since it should not be due to the
reason of combining >100 pep.xml files on the command line. Thanks for
your help too, Brian.


Bernard

On Jul 3, 2:24 am, David Shteynberg <dshteynb...@systemsbiology.org>
wrote:

> What was the problem with the final generated interact.pep.xml file?
> Can you verify that all of your pep.xml files are complete?  Check
> their size and starting and ending tags for completeness.  If there
> are any error message please post them here.
>
> -David
>