How could I run PTMProphet correctly?

[JWang Lu]

I have already got pepXML from .dat file and finished  iProphet. But when I wanna analyse PTM for next step, I got an error like this:

Unknown file type. No file loaded.d:/TPP/data/20210119/mascot/F006127_AIBI.(null) ERROR: cannot read scan in data file d:/TPP/data/20210119/mascot/F006127_AIBI.(null) exiting ...

I choosed the file `d:/TPP/data/20210119/mascot/interact.ipro.pep.xml` to analyse, which could be open correctly. But I don't know why the log tell me `F006127_AIBI.(null)` is wrong. `F006128_AL0A.pep.xml` is the name of my pepXML.

Besides, when I processed topepxml, I had met the warning(cannot open "" for reading MS instrument info.) and I could not open ion spectrum until I extract the .dta and .out manually from tar. I don't know if these two thing are related. I have already tried to move the .dta file to the same folder as pepXML, but the error still.

Thanks for your generous help  :)

JWangLu

[My Error Log]

[PTMProphet Setting]

[David Shteynberg]

Dear JWangLu,

This message would come up when the software tool attempts to read the mzML file that is referenced by the pepXML file.

It appears that your input pepXML file is not correctly referencing the mzML data file.  Perhaps the issue is with the file paths, I am not sure without looking at the file.  

If you can check the pepXML file for  msms_run_summary tags and verify they are pointing to existing files.  

For example, for files: 

  c:\TPP\data\class\Yeast\data\OR20080317_S_SILAC-LH_1-1_01.mzML 

  c:\TPP\data\class\Yeast\data\OR20080320_S_SILAC-LH_1-1_11.mzML 

msms_run_summary entries should look like this:

 

> grep "<msms_run_summary" interact.pep.xml

<msms_run_summary base_name="c:\TPP\data\class\Yeast\data\OR20080317_S_SILAC-LH_1-1_01" msManufacturer="UNKNOWN" msModel="UNKNOWN" raw_data_type="raw" raw_data=".mzML">
<msms_run_summary base_name="c:\TPP\data\class\Yeast\data\OR20080320_S_SILAC-LH_1-1_11" msManufacturer="UNKNOWN" msModel="UNKNOWN" raw_data_type="raw" raw_data=".mzML">

Cheers,

-David

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