Confidence is not calculated - does not find the decoys

[Carlo de Oliveira Martins]

Hi all,

As shown in the attachment, there is no result for protein and peptide confidence in my results.

I am using the latest version of Peptide Shaker (1.16.44) and SearchGUI version 3.3.17 to process data.

My fasta file originally did not contain decoy sequences, so I used the built-in tool from the SearchGUI to add decoys (with the automatic suffix '_REVERSED').

However, when I load the results into a new project, I get a warning that my database contains no decoys, so the confidence will not be calculated.

Any thoughts?

(my first time using this tool, so I may be doing something really dumb)

Thank you,

Carlo

[Harald Barsnes]

Hi Carlo,

It seems like you are using some sort of custom protein sequence database? In that case, it may be that the decoy sequences are not added or picked up correctly.

Have you tried clicking any of the yellow warning icons at the right-hand side of the protein table? This may give you a bit more information about what is going on.

If you are willing to share your database I can always have a closer look as well?

Best regards,

Harald

[Carlo de Oliveira Martins]

Hi Harald,

Thanks for your quick response.

This is what I get when clicking on the yellow warning signs:

You are correct. I am working with a non-Uniprot database (attached here the output from PeptideShaker, with decoys), actually, with more than one, and this is happening with al of them.

Best wishes,

Carlo

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[Carlo de Oliveira Martins]

Sorry, I actually added the wrong database...

[Harald Barsnes]

Hi Carlo,

As expected the problem is the non-standard headers. Please see our help page for how to reformat custom headers in order to make them compatible with PeptideShaker: https://github.com/compomics/searchgui/wiki/DatabaseHelp#non-standard-fasta.

Hopefully a bit of easy search and replace in the target FASTA file should allow you to use the add the decoys in SearchGUI without any errors.

Best regards,

Harald

[Carlo de Oliveira Martins]

Thank you!

Best regards

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