Interfering protein and PI status and number of PTMs

[GoogleCodeExporter]

Hi.

I use peptide shaker to (in addition to "normal" proteomics) to also search my 
standard synthetic peptides and other known small peptides not necessary from 
proteins. I do this by adding them as new proteins in a normal FASTA file. In 
previous versions this worked out very nicely, no problem at all. However, in 
you latest version (0.21.0) this is no longer possible as I during import of 
data to Peptide Shaker I get a error message stating "Resolving protein 
inference status, inferring peptide and protein PI status" - "Importing data 
canceled". I guess that this is somehow due to me finding the whole "protein" 
in one peptide.  Do you have any solution to this?

regarding another issue: can shaker and/or search gui only handle up to 3 PTMs 
pr peptide. The last version I tried this on was 18.something, due to the error 
of importing data where the peptide and the protein is the same...

Please contact me off line if more details are required

best,
Terkel

> What steps will reproduce the problem?

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

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

> 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 terke...@gmail.com on 4 Jun 2013 at 11:51

Attachments:

• Shaker.png

[GoogleCodeExporter]

The problem is the parsing of the protein headers in the database. See 
http://code.google.com/p/searchgui/wiki/DatabaseHelp for how to set up a valid 
database for SearchGUI.

As for the limit on the number of modifications per peptide, this was a bug in 
our use of X!Tandem that was fixed in SearchGUI v1.11.0.

Let me know if you need more help.

Original comment by harald.b...@gmail.com on 4 Jun 2013 at 2:59

• Changed state: Fixed