X!Tandem search fails in TPP 5.0.0

sudip ghosh

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Jul 30, 2019, 11:15:27 AM7/30/19

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Hi All,

I am trying to search some mzML/mzXML (converted from .wiff) files in X! Tandem but it fails repeatedly (RETURN CODE:65280, 256). While the same set of mzML file was searched successfully in Comet. I am attaching the param file. Please help me out.

Regards,

Sudip

XTandem error.png

tandem_params.xml

David Shteynberg

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Jul 30, 2019, 2:30:38 PM7/30/19

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Hi Sudip,

Based on the message it appears that your fasta database may contain amino acid letter codes that make Tandem fail. Can you check your fasta database to make certain it contains only valid protein sequences?

Thanks,

-David

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sudip ghosh

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Jul 31, 2019, 1:56:55 PM7/31/19

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Hi David,

Thanks for the suggestion. I also suspected the same and currently doing the manual check. However, as I said, Comet did not report any error! My other query is, which format should I take as raw data (mzML/mzXML) as search input and how much it differs in terms of peptide identified (pep.xml)? I also need to combine the result of comet and tandem after that.

Thanks,

Sudip

On Wednesday, July 31, 2019 at 12:00:38 AM UTC+5:30, David Shteynberg wrote:

Hi Sudip,

Based on the message it appears that your fasta database may contain amino acid letter codes that make Tandem fail. Can you check your fasta database to make certain it contains only valid protein sequences?

Thanks,
-David

On Tue, Jul 30, 2019 at 8:15 AM sudip ghosh <sgblac...@gmail.com> wrote:

Hi All,

I am trying to search some mzML/mzXML (converted from .wiff) files in X! Tandem but it fails repeatedly (RETURN CODE:65280, 256). While the same set of mzML file was searched successfully in Comet. I am attaching the param file. Please help me out.

Regards,
Sudip

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