I finnaly find how to interrogate dabases/ spectra with unspecific leavage on SearchGUI. Nevertheless, the output files were not read by Proline. When I tried to import it, I have this error message : code 32002"reqirement failed : unexpected number of enzyme"
Is there an additional action to do on proline to authorize the search?
Thanks a lot,
Sorry I started to answer yesterday to your first question but I didn't finish...
Concerning SearchGUI, we don't use it but you finally found how to do! What is the format of the result file? Is it an mzIdent ML file? Which search engine do you use with Search GUI?
It seems that we are too restrictive for search engines other than Mascot, since we require for all other search engines that a single enzyme has to be used.
This requirement is only applied during the computation of the number of peptide missed cleavages.
We have to patch the current version of Proline to set this number to zero when no enzyme is used. This should allow to import such produced result files.
We will need also to verify our side if there is no other blocking point.
We can try to do a similar search on our side, or better, if you can, please share by email a file you would like us to test.
Thank you for your answer,
I will send you a .xml by email. And if I anderstand well, if you can import it by your side, we will need to update Proline version.
Is the update easy? Our old projects in proline will not be erase by the update?
For a follow up : a fixe has been done and will be included in next version.