Problems : converting ~.dat and ~.sqt to pepxml

[Hoikeun Jeong]

Hi there,

I have problems converting ~.dat and ~.sqt to pepxml at TPP.

First, I learn convert mascot ~.dat files to ~.pepxml and running TPP. Those ~.dat files are gotten with decoy data. But at TPP, the result files have errors, not opened.

Second, I have no idea convert ~.sqt files to pepxml. I selected Sequest mode in web based TPP. But at pepxml tab, I cannot add ~.sqt files. It only shows "`.Directory with .out files to convert to pepxml". Where can I find ~.sqt file converter?

Thank you

[Luis Mendoza]

Hello,

You can convert .sqt files to PepXML by using the command-line: "Sqt2XML myfile.sqt".  We will add this option to the interface for the next release.

What errors do you see with your Mascot .dat files?  Do note that you need to have a copy of the same database that you searched against present in a directory accessible by TPP.

Cheers,

--Luis

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[Hoikeun Jeong]

Thanks Luis

But I have another problems ;

In sqt things, I got pepxml files with your suggestion and apply pepxml files to 'analyze peptides'.

But the results show 'Command failed' Return code : 256

In command windows, all result shows repetedly

file 1: ~name.pep.xml

Unknown file type. No file loaded.

WARNING: cannot open data file ~path. unknown in msms_run_summary tag... Unknown file type. No file loaded.

WARNING: cannot CORRECT data file ~path. unknown in msms_run_summary tag...

Also, in mascot ~.dat paptide analyze things repeatedly show ;

Warning: could not find scan numbers of spectrum File: name.mzXML Scans:1507 RT:15.8351min Charge:2 Fragmentation:cid

Set to 0000

can you reply please?

Thank you,

Hoikeun

[Luis Mendoza]

Hello Hoikeun,

Are there any errors or other messages when you convert the .sqt files to .pep.xml ?  Are all files in the same directory along with the .mzML files?

As for the Mascot files, make sure you follow the following process to make sure that the .dat files are compatible with TPP:

1. .raw file to mzML (or mzXML)  ==> myRun.mzML
2. Convert this file to mgf (using MzXML2Search) ==> myRun.mgf
3. Use this file as an input to MASCOT; MASCOT then generates .dat
file ==> F0123456.dat
4. Rename this to the original base name ==>  myRun.dat
5. Convert to pepXML  ==> myRun.pep.xml
6. Analyze with PeptideProphet, etc.

Cheers,

--Luis

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