x!tandem point mutations

[Maik Boehmer]

Hi,

for mass spec analysis of an unsequenced organism we are using X!tandem to search against the FASTA database of a related organism allowing for point mutations in refinement mode. After transformation of the tandem.xml search results to pep.xml, peptides containing point mutations are still present but are shown with the wrong sequence information (the one from the FASTA file, point mutation not considered) and masses. Is there any way that peptides containing point mutation are shown also in the pep.xml file with an annotation marking them as mutated or preferentially with the correct sequence information.

Thanks.

[Jimmy Eng]

I'm not aware of any way to do what you want to do. And
realistically, support for this probably isn't going to occur anytime
soon just because it's not an analysis that's commonly done.

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