Limit of iProphet

[Rachel]

1. I tried to combine large number of files (~1000) using iprophet. I
tried using command line as well as the tpp-gui. but failed.
The error message is,
This application has requested the runtime to terminate in an unusual
way. Please contact the application's team for more information.

2. Then I split the 1000 files into 12 batches and combine the
peptideprophet of these files using iprophet. Then I tried to combine
these 12 large iprophet files in iprophet, also failed. I got the same
error message.

Is anyone know the limit of iProphet?

thanks a lot.

[David Shteynberg]

Hi Rachel,

It is limited only by the amout of memory you have on your system.
The memory req scales linearly with number of spectra being combined.
Obviously the more spectra that are analysed together the better the
statistics are going to be, but this too has a practical limit. Once
you have the individual iProphet pepxmls you should not run iProphet
on them again since you'll run into the same memory issue. Instead
this is a perfect time to run ProteinProphet on the iProphet files and
specify the IPROPHET option to make sure it uses iProphet
probabilities.

-David

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[Rachel]

Hi David,

Thank you very much!

Rachel :)

On Sep 30, 2:46 am, David Shteynberg <dshteynb...@systemsbiology.org>
wrote:

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