Not loading mzID files appropriately from SearchGUI to Peptide Shaker.

[GoogleCodeExporter]

> What steps will reproduce the problem?

We tried to use peptide shaker to load these files:

http://mingwangbeta.ucsd.edu/public/jakob/20150529_Fuji_MR_JH_Biofilm00H.mgf
http://mingwangbeta.ucsd.edu/public/jakob/20150529_Fuji_MR_JH_Biofilm00H.msgf.mz
id
http://mingwangbeta.ucsd.edu/public/jakob/Daw3_edited_concatenated_target_decoy.
fasta

after searching with your search tool using MSGF+

> What is the expected output? What do you see instead?

We expected there to be some IDs in the mzid but it said there were none. 

Thu Aug 13 13:02:45 PDT 2015        No PSM found in 
20150529_Fuji_MR_JH_Biofilm00H.msgf.mzid.
Thu Aug 13 13:02:45 PDT 2015        No identifications retained.

> What version of the product are you using? On what operating system?

Peptide Shaker Downloaded 8/13/2015. Windows 7 64-bit. 

> Please provide any additional information below.

> If the reported issue resulted in the tool crashing, please
> also upload the file called PeptideShaker.log (found in the
> PeptideShaker-X.Y.Z\resources folder).

Original issue reported on code.google.com by mwan...@gmail.com on 13 Aug 2015 at 8:08

[GoogleCodeExporter]

Thanks for telling us about this. Could you also provide your search parameters 
file so that we can try to reproduce the issue on our side?

Original comment by harald.b...@gmail.com on 14 Aug 2015 at 10:33

• Changed state: Accepted

[GoogleCodeExporter]

I don't need the search parameter file after all. The problem turned out to be 
that our mzIdentML parsing code was not able to parse mzIdentML files where 
there were no post-translational modifications. This has now been fixed and a 
new PeptideShaker version will be released as soon as possible.

Original comment by harald.b...@gmail.com on 14 Aug 2015 at 12:02

[hbarsnes]

PeptideShaker v1.0.0 has now been release which should fix this problem. If not please let us know and we'll reopen the issue.