Mascot DTA to Pepxml

[Dhruti]

I tried to convert Mascot DTA to pepXML using MASCOT2XML program
without any success. I get following error

c:/Inetpub/wwwroot/ISB/data/F002856.pep.xml [ Unreadable! ]
c:/Inetpub/wwwroot/ISB/data/F002857.pep.xml [ Unreadable! ]

un_in c:/Inetpub/wwwroot/ISB/data; c:\Inetpub\tpp-bin\Mascot2XML c:/
Inetpub/wwwroot/ISB/data/F002856.dat -Dc:/Inetpub/wwwroot/ISB/data/
dbase/uniprot_trembl.fasta -pI -Etrypsin -notgz -desc -shortid

command "c:\Inetpub\tpp-bin\Mascot2XML c:/Inetpub/wwwroot/ISB/data/
F002856.dat -Dc:/Inetpub/wwwroot/ISB/data/dbase/uniprot_trembl.fasta -
pI -Etrypsin -notgz -desc -shortid" failed: Unknown error

Command FAILED

THe Dta was generated by searching thermo raw files using MASCOT
2.3.

THanks

[Luis Mendoza]

Hello,
I am not sure if this is the source of the error, but the recommended
procedure to process MASCOT data with the TPP is the following:

1. Convert Thermo .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.

Let us know if this does not work. Also, what version of the TPP are you using?

Cheers,
--Luis

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[Vidya Venkatraman]

Hi Luis,

I just had a question about using converting Mascot data to pepxml in TPP. I was able to successfully convert Mascot generated .dat files to pepxml using TPP gui. Though, i was wondering if having mzXML within the same folder structure is mandatory. Will the process work without mzXML? Also, can we use mgfs instead of mzXML within the same folder structure to convert .dat to pepxml.

Thanks

Vidya

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[kshitiz tyagi]

Hi,

I think you dont need to convert mascot .dat files to pepxml using Mascot2XML, you can directly run xinteract which takes care of the conversions. It should go something like:

xinteract -D/full/path/database -e(enzyme; T for Trypsin) (generaloptions) -O(prophetoptions) -Noutput.pep.xml summary1.dat summary2.dat....

I generally have the mzXML files in the same directory or I make a soft link in the search directory pointing to the original mzXML files. I dont think you can have mgf files because, if I am not wrong, mgf files dont store MS info.

I am fairly new with TPP so apologies if I have said anything wrong. Also note that I use the linux version of TPP.

Cheers,

Kshitiz

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[Vidya Venkatraman]

Hi Kshitiz,

Thanks for your prompt response. Actually I dont have the mzXML files. I just have the mgf files using which I ran Mascot and got the .dat files. Now i want to convert the .dat files to pepxml. I was wondering if it is possible for me to convert the .dat files to pepxml with the mgfs. Right now, I have to separately convert the .raw files to mzXML to get TPP to convert .dat to .pepxml. I was wondering if I could do so without actually having the mzXMLs.

Thanks
Vidya

On Wednesday, July 25, 2012 11:43:25 AM UTC-4, kshitiz wrote:

Hi,

I think you dont need to convert mascot .dat files to pepxml using Mascot2XML, you can directly run xinteract which takes care of the conversions. It should go something like:

xinteract -D/full/path/database -e(enzyme; T for Trypsin) (generaloptions) -O(prophetoptions) -Noutput.pep.xml summary1.dat summary2.dat....

I generally have the mzXML files in the same directory or I make a soft link in the search directory pointing to the original mzXML files. I dont think you can have mgf files because, if I am not wrong, mgf files dont store MS info.

I am fairly new with TPP so apologies if I have said anything wrong. Also note that I use the linux version of TPP.

Cheers,

Kshitiz

[Mariarita Arenella]

Hi,
thank you, I did it and it worked I can open the file and I can see the list of peptides etc., but my pep.xml file doesn't work in generating pep 3d image showing the precursor ions recognized by the instrument.Have you ever used this tool? Have you ideas?
Thanks again,
Mariarita

2012/7/25 Vidya Venkatraman <vidya....@gmail.com>

On Friday, July 22, 2011 3:33:09 PM UTC-4, Luis Mendoza wrote:

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