parsing error for pepXML from mascot result

[andreas quandt]

dear list,

i analyzed a few samples with mascot and converted the dat file
successfully to pepXML (only error: scan number cannot be found).
afterwards i was running xinteract on all created pep.xml files
(arguments: l -dDECOY_ -OAlIwp).
this was also successful but when i want to display the results, i get
an error message:

*unable to read pepxml file: error parsing pepxml file: XML parsing
error: mismatched tag, at xml file line 1048198, column 2

when looking at the file, the line contains following tag: </search_hit>.
the same happens when using iprophet. here the error message is the same
and when jumping to the indicated line, the same tag appears.

does anyone of you know what's going wrong and/or know how to fix this?

many thanks in advance,
andreas
*

[andreas quandt]

dear list,

i analyzed a few samples with mascot and converted the dat file
successfully to pepXML (only error: scan number cannot be found).
afterwards i was running xinteract on all created pep.xml files
(arguments: l -dDECOY_ -OAlIwp).
this was also successful but when i want to display the results, i get
an error message:

unable to read pepxml file: error parsing pepxml file: XML parsing

[Brian Pratt]

What version of the software are you using?

Brian

[andreas quandt]

hey brian,

its 4.2.1 in that case ;-)

[Brian Pratt]

Perhaps you could upload the .dat file to ftp://insilicos.serveftp.net/pub
and I can investigate. Zip it up with the database you used, and the mzXML
file (so, everything needed to run xinteract).

[Etienne Caron]

Dear Brian, 

I'm a postdoc in Ruedi Aeberold's group. I have the exact same problem as posted by Andreas in 2009. 

Here is the error message I get when I run xinteract from comet search results: 

unable to read pepxml file: error parsing pepxml file: XML parsing error: mismatched tag, at xml file line 10931001, column 2

Do you know how I can fix this problem?

Thanks in advance for your help. 

Best regards, 

Etienne 

[David Shteynberg]

At least one of the input files pepxml is incomplete.  Check the file sizes.  Which version are you on?

-David

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[Etienne Caron]

Dear David, 

Thanks! Indeed, one of the files was incomplete. Now it works!

Best, 
Etienne

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