Problem with PTMprophet

[felipe velasquez]

hello again

I am trying to analyze some samples from thermo raw data, but I cannot find any results. However, another person analyzed the same data using another platform and found some results. Is this normal?

Felipe

[Luis Mendoza]

Hello Felipe,

It is in general not normal to not find "any results" with TPP when other platforms do find some, as there is often partial, if not significant, overlap.  Typically when no results are found, it points to either bad data (presumably not in this case) or incorrect parameters (including choice of database if doing sequence searching).

For your specific case, we would need to know more specifics if you are looking for help in your TPP analysis -- e.g. what kind of data you have, what components are you using, what parameters were set, etc.

We do note that in some instances other software does tend to inflate the number of results provided to the user, albeit with either a very high or otherwise poorly characterized error rate.

Again, without knowing specifics, it is impossible to tell what could be going on.

Cheers,

--Luis

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[felipe velasquez]

Hello luis, thanks.

This is one of the messages... there is something I can do to fix it?

Thanks again,

Felipe

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[Luis Mendoza]

Hello Felipe,

The top message seems to indicate a permissions error; perhaps the files under /tmp are not accessible to the Apache/web user?  Since this looks like a Linux install, it depends on how that part of your system is set up.

The large error may or may not be related to the previous one, but it is telling you that the pepXML file is not valid PepXML.  There can be many reasons for this, so it depends on how that file was initially generated.

What steps did you take to go from your Thermo raw file to this pepXML?   Do you get any other errors or warnings before this step?  Have you been able to run other data as a test of your TPP install?

Cheers,

--Luis

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[felipe velasquez]

Thanks Luis for your quick response. Finally, I could resolve the problem. As a beginner user, I made a mistake with Comet params. Thanks again for your attention and support.

kind regards,

Felipe

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