PepXML viewer

[research user]

Why do I get this message when I try to open the peptide prophet results in PepXML viewer

 

error: error with html display: XML parsing error: mismatched tag, at xml file line 4, column 2

 

how can it be taken care of

 

Kanchan

[Luis Mendoza]

Hello Kanchan,
Is this happening with only a specific file, or with several/all?

This error message is not very specific for us to debug. Can you
please open this file in a text editor (e.g. Wordpad) and examine
the contents of line 4? One possibility is that there might be a
non-standard character messing up the xml parsing. Also, make sure
that the file 'looks' like a good xml document, and that it is
more than just 4 lines long!

Finally, Josh suggests that this might be a permissions issue. The
PepXMLViewer needs to write a temporary file in that directory, so
make sure that the directory has the appropriate permissions.

Hope this helps,
--Luis

research user wrote:
> Why do I get this message when I try to open the peptide prophet results
> in PepXML viewer
>
>
>
> error:
>

> *error with html display: XML parsing error: mismatched tag, at xml file
> line 4, column 2*

[research user]

Hi Luis,

 

I could open up other xml files but this one which is a result from peptide validation is showing this error. To me it looks like a good xml file (I dont have much experience with xml). Here I have attached the file for you to have a look. It will be a great help if u can explain to me what is going wrong. I think permission should not be a problem as the results are stored in the

 

C:\Inetpub\wwwroot\ISB\data folder as needed by tpp.  Also I can see other files with .xsl, .index and .xls created in the same folder after the analysis with peptide prophet. Your guidance will help in understanding xml files and future trouble shooting of them.

 

thanks

 

Kanchan

 

[Luis Mendoza]

Hi Kanchan,
I was able to open your file using the PepXMLViewer on our system.
The file looks fine, xml-wise. What version of the TPP are you using?

(The PepXMLViewer version can be found at the bottom of the web page
when you open any file.)
--Luis

[research user]

Hi Luis,

The version which I am using at the moment is TPP v3.4 SQUALL rev.1, Build 200801311151. I am using the GUI interface of TPP ( petunia). I installed the version from http://tools.proteomecenter.org/wiki/index.php?title=TPP:Windows_Cygwin_Installation.

Is there any other latest version avialable, where can I download it from.

Thanks

 

Kanchan

[research user]

Hi Luis and Josh,

In the previous mail you mentioned about the permission problem with pepxml viewer, what is this issue and how it can be resolved.

Kanchan