Importing Mascot.dat results

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What steps will reproduce the problem?
1. Loading a Mascot.Dat file into peptide shaker
2.
3.

What is the expected output? What do you see instead?
Expect identifications from the Mascot.dat file to be carried into peptide 
shaker but none are retained.

What version of the product are you using? On what operating system?
PeptideShaker 0.9.3 with Windows 32 bit OS

Please provide any additional information below.

I have recently installed peptide shaker and I can get this to work
well with X!Tandem and OMSSA results generated in SearchGUI, however I
am having issues with importing Mascot results.  Whenever I add a
Mascot.dat file no identifications are carried into peptide shaker.
Do you have any helpful ideas or suggestions?

Many thanks 

Original issue reported on code.google.com by aad100%y...@gtempaccount.com on 3 Oct 2011 at 2:23

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Compatibility with Mascot is indeed a bit more complicated than with OMSSA and 
X!Tandem.
First, you need to ensure that the same fasta file was used. Remember to turn 
off the "decoy" option but rather use the same concatenated target/decoy 
database as with SearchGUI. Also verify that all identification options are the 
same.
Then in the "open" dialog of PeptideShaker, click on "Edit" after Search 
Parameters and verify that all the modifications used for the search are 
selected in the "Expected Variable Modifications".

If the problem persists can you send us the log file located in the "conf" 
folder of PeptideShaker together with the problematic dat file?

Original comment by mvau...@gmail.com on 3 Oct 2011 at 3:30

• Changed state: Started

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I have tried to keep all the search parameters identical, and the data have 
been searched against the same concatenated target/decoy database, but no 
results are imported.

I have attached some BSA example data and the log file as requested.  You 
should have all the files you might need to repeat the problem. The only thing 
ommitted is the FASTA file.  I used a recent (less then one week old), version 
of the bovine data on UniProt if you would like to download this yourself.

Please let me know if there is anything else you need.

Many thanks for your help

Original comment by aad100%y...@gtempaccount.com on 3 Oct 2011 at 3:54

Attachments:

• BSAa.zip

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Thank you very much for uploading the data. 
If you look at your dat file, you will see that protein accessions are not 
retrieved properly. For example line 6146 the accession retrieved is 
"P02769|ALBU_BOVIN" instead of "P02769". I guess you see the same problem in 
the Mascot summary. PeptideShaker thus looks for the accession 
"P02769|ALBU_BOVIN" in Uniprot and does not find it, hence no identification is 
retained.
It seems that your fasta parsing rule is not properly configured for uniprot on 
your Mascot server. Please refer to 
http://www.matrixscience.com/help/seq_db_setup.html for database setup in 
Mascot. Hopefully with the correct parsing rule you will be able to load your 
dat file together with the other files. 

Original comment by mvau...@gmail.com on 4 Oct 2011 at 8:28

• Changed state: Accepted
• Added labels: Type-Other
• Removed labels: Type-Defect

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I have changed the parsing rules on the Mascot server and it all works 
perfectly.  Many thanks for your help.

Original comment by aad100%y...@gtempaccount.com on 4 Oct 2011 at 12:44

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Original comment by harald.b...@gmail.com on 4 Oct 2011 at 12:50

• Changed state: Fixed