tpp2mzid help - 'no peptide evidence found ...'

[Alastair Skeffington]

I'm at the end of a multi-year odyssey of a project, and I just need to submit data to PRIDE.

Unfortunately, when I run tpp2mzid for some prot.xml files, I get an error such as this:

Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from Br20418.t2

This only happens for some prot.xml files, but I'm not sure why. The pep.xml files from which the prot.xml are derived convert fine.

I've put an example here: https://we.tl/t-Z9qNNjDC0k

I was running TPP via the docker container: digitalproteomes/tpp:version-5.2.0.1

Here is the stdout in full:

Reading: HCLC_EhN.prot.xml

Reading: /data/HCLC_EhN_ipro.pep.xml

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

Unknown xx modification: B = 114.535 42.5515

Unknown xx modification: J = 113.084 44.0023

Unknown xx modification: O = 237.148 80.0613

Unknown xx modification: U = 150.954 6.13277

Unknown xx modification: X = 111 46.0864

Unknown xx modification: Z = 128.551 28.5358

17648 psms read.

Warning (A), no peptide evidence found for (mod): EENAFVQKIAE from Br20418.t2

Help would be very much appreciated!

Thanks,

Alastair

[Michael Hoopmann]

Hi Alastair,

There is a much newer version of tpp2mzid in our current release candidates of TPP version 6. I’m hoping that the error messages have been resolved in this new version. However, I also need the fasta search database file to run the conversion with the newer tpp2mzid. Could you also provide a link to that file and I will finish my tests and let you know the result?

Thanks,

Mike

 

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[Alastair Skeffington]

Hi Mike,

Thanks for getting back to me so quickly. Here's the database: https://we.tl/t-wZsZ3uSq1r

Is version 6 available as a container? I've never managed to install TPP properly on a linux machine ...

Alastair

[Eric Deutsch]

I have not yet created a container for 6 but I should. I could try to do that soon if there is demand to use it/test it.

 

Thanks,

Eric

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[Alastair Skeffington]

Hi Eric,

Very happy to test it!

Thanks,

Alastair

[Michael Hoopmann]

Hi Alastair,

I can definitely reproduce the error, which is caused by the presence of two identical fasta databases in your search space. I’ll need some time to fix the bug and report back to you.

Cheers,

Mike

 

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[Alastair Skeffington]

Hi Mike, 

Thanks for looking into it! I'm not quite sure I understand ... all IDs in the database (and therefore search space?) are unique - do you mean two identical databases in the file system were somehow used at different points? Is there any quick fix I can apply by editing the xml file, if it's going to take you a while?

Cheers,

Alastair

[Michael Hoopmann]

Hi Alastair,

Yes, you can try this workaround and it should convert:

 

1.       Open up your ipro.pep.xml file in a text editor

2.       Find and replace all instances of “../../../../Databases/EhuxAllproteins_MCC_decoy.fasta” with “../../Databases/EhuxAllproteins_MCC_decoy.fasta”

3.       Save the file and then run tpp2mzid on your prot.xml file

 

I would suggest you make a backup of your ipro.pep.xml file first. Keep the backup under a different file name; do not change the name of the ipro.pep.xml file that you are altering. The bug was that you used the same fasta file from two different locations in your searches, and therefore the converter assumes that they are two different databases. It then gets confused later when all the protein entries in each database are identical (which is the bug I have to fix). Simply pointing all fasta files to the same location fixes your problem.

 

Cheers,

Mike

 

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[Alastair Skeffington]

Hi Mike,

Great - yes making sure all database references in the pep.xml match the reference in the prot.xml exactly fixes it.

Thanks for your help!

Alastair