New at TTP. Problem with PSM validation

[Carlos Humberto Paván]

Dear all

I have recently installed TTP 5.2 and I´m still learn about it. I´m stuck at the peptide validation process: I get the follow error next to run Peptide Prophet:

"Initialising statistical models ...

command "C:/TPP/bin/PeptideProphetParser "/tmp/a04412/params/interact.pep.xml" MINPROB=0.0 CLEVEL=-1 PPM MALDI" failed: Unknown error

command "C:/TPP/bin/PeptideProphetParser "/tmp/a04412/params/interact.pep.xml" MINPROB=0.0 CLEVEL=-1 PPM MALDI" exited with non-zero exit code: 255

QUIT - the job is incomplete"

The data is from a 4800 MALDI, a single spot from gel.

Regards and Thanks

[Carlos Humberto Paván]

In some opportunities, I have had a value of 0 in the probability column after the peptide prophet run

[David Shteynberg]

Dear Carlos, 

There is probably some bug exposed by the modeling of this type of data with the specific set of options you enabled.   If you are able to share a part of your dataset that can replicate the issue, I am able to troubleshoot this  further. 

Thanks,

David

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[Carlos Humberto Paván]

Dear David

Thank you your answer and your offer. Of course I can send you the dataset. I have attached it. You will note this is a small number of spectrums.

Looking forward your comments

PS I have attached the interact file too with the 0 prob result.

El lunes, 20 de julio de 2020, 13:29:42 (UTC-3), David Shteynberg escribió:

Dear Carlos, 

There is probably some bug exposed by the modeling of this type of data with the specific set of options you enabled.   If you are able to share a part of your dataset that can replicate the issue, I am able to troubleshoot this  further. 

Thanks,

David

On Sat, Jul 18, 2020, 12:10 PM Carlos Humberto Paván <charl...@gmail.com> wrote:

Dear all

I have recently installed TTP 5.2 and I´m still learn about it. I´m stuck at the peptide validation process: I get the follow error next to run Peptide Prophet:

"Initialising statistical models ...

command "C:/TPP/bin/PeptideProphetParser "/tmp/a04412/params/interact.pep.xml" MINPROB=0.0 CLEVEL=-1 PPM MALDI" failed: Unknown error

command "C:/TPP/bin/PeptideProphetParser "/tmp/a04412/params/interact.pep.xml" MINPROB=0.0 CLEVEL=-1 PPM MALDI" exited with non-zero exit code: 255

QUIT - the job is incomplete"

The data is from a 4800 MALDI, a single spot from gel.

Regards and Thanks

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[David Shteynberg]

Hi Carlos,

The TPP is statistical software that takes advantage of statistical trends in data and requires many data points to work well.  Do you have a dataset of reasonable size with maybe dozens or hundreds of spectra?  Also can you post the file somewhere I can download it?  Sending files as email attachments may not work for larger files.

Thanks,

-David

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[Carlos Humberto Paván]

Dear David

Thank you for your answer!, My question was regards this kind of data  from MALDI, with no a huge number of spectra. I have diffent dataset but I think my specific question was answered with you explanation.

Thank you again I´m sure I will have more doubts in the future.

Regards

Carlos

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