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Immortalin / peptide-shaker

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error in PTMs scoring PeptideShaker #54

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
> What steps will reproduce the problem?
loading of data after SearchGUI to peptideshaker 

> What is the expected output? What do you see instead?
found less D-scores than PTMs for modification of mass 42.0106 in peptide 
TALKLLTIDNRVTLISF in spectrum ......

> What version of the product are you using? On what operating system?
r-0.34.0
Windows 7 Prof.

> Please provide any additional information below.
We perform a search aginst 3 proteins with a lot of variable modifications 
(acetylation, propionylation, oxidatin, phosphorylation etc.)

> 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 Oleksand...@gmail.com on 7 Oct 2014 at 8:51

GoogleCodeExporter commented 9 years ago 
Hi and thank you for reporting this issue. 
It looks like the software was confused by the setup you used. Can you make the 
data available to me (mvaudel@gmail.com) so that I see what went wrong?
I would need the mgf and fasta files as well as the search parameters.
Best regards,
Marc

Original comment by mvau...@gmail.com on 7 Oct 2014 at 9:44

GoogleCodeExporter commented 9 years ago 
Hi Marc,
I just have sent files to you by e-mail.
Thank you for your help.
Best regards,
Alex

Original comment by Oleksand...@gmail.com on 7 Oct 2014 at 9:59

GoogleCodeExporter commented 9 years ago

Original comment by harald.b...@gmail.com on 13 Oct 2014 at 5:01

GoogleCodeExporter commented 9 years ago 
The new just released PeptideShaker version (v0.35.0) is now able to load this 
dataset.

Note that in order to search with unspecific cleavage the enzyme called 
"unspecific" (previously called "no enzyme") ought to be used. "Whole protein" 
(and "Top-down"), as was originally used for this dataset, means no cleavage at 
all, i.e., compare against the whole protein sequence.

If you still have problems loading your data please let us know and we'll 
reopen the issue.

Best regards,
Harald

Original comment by harald.b...@gmail.com on 23 Oct 2014 at 8:37