Loading searched peptide prophet files on Pep3d Viewer

[Vidya Venkatraman]

Hi,

I have received searched Xtandem data (from 1 raw file) which was also run through peptide and protein prophet. I am trying to open the iprophet pep.xml file through TPP in the pep3d viewer. But when i click on generate 3d image, it errors saying could not open input file. Also, you can see how the mzxml does not appear such that it can be selected. 

I just wanted to check on how one can import iprophet pep.xml results onto pep3d viewer if it was searched and run through peptide prophet elsewhere. I do have the fasta, mzxml, pep.xml, ipep.xml, prot.xml under C:\Inetpub\wwwroot\ISB\data\data.

Could it be the naming convention eg. the files need to have the same name? What files does it look for or what files do i need to have for this to work?

Lastly, when i took the pep.xml file and ran it through peptide prophet on the TPP gui (instead of starting with the ipep file), it does seem to work and generate the pep3d image. 

I dont use TPP that often, so this could be something obvious. But i appreciate any guidance on this matter.

Thanks in advance, 

Vidya

[Luis Mendoza]

Hello Vidya,

It seems that your iProphet file might contain incorrect/incomplete
file paths for the source mzXML files. What steps did you follow to
generate this file? Feel free to email it to me so I can further
diagnose.

As you found out, you can always just open the PeptideProphet results
file in Pep3D, or the mzXML/mzML raw data.

Cheers,
--Luis

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[Vidya Venkatraman]

Hi Luis,

Thanks for your response.

I have encountered another issue now wherein if I try to convert a mascot .dat file to pepxml, it does the conversion and when I try to use this pepxml  to run peptideprophet and proteinprophet, it fails. Please find attached the screenshot and error log for the peptide prophet command.

I tried to check if .dat to pepxml conversion worked properly, but realised that when I click on the pepxml, nothing loads on the pepxml viewer and I also saw that usually there is a index file that is created and in this case, it did not create the index file as well. Please also find attached the screenshot and log of the pepxml conversion command. Just to make sure the .dat file is good, i was also able to open it up on Scaffold and see some proteins.

I am unable to attach the .dat,.mzxml,.pep,.fasta here. Is there another way I could send it to you? Or are the logs sufficient to debug what could have gone wrong.

Thanks in advance,

Vidya