Semi-Cleavage

support
Semi-Cleavage Vera  2017-10-10 14:22
 
Hi Skyline team,

I know you have already update an "allow Semi-Cleavage" section for enzyme in Version 3.7. However, it doesn't really work because although I clicked the option in enzyme edit, nothing changed and if I click the enzyme I just edit, the option was shown not checked at all. It looks like skyline can't remember or recognize the setting. Could you help figure out what happened?

Thanks a lot.
Vera
 
 
Brendan MacLean responded:  2017-10-10 14:32
Hi Vera,
Thanks for reporting this. I see what you mean. I will fix this in the next Skyline-daily.

Skyline does support a Trypsin (semi) by default, which I have been using succesfully just very recently. Are you looking for something other than Trypsin?

--Brendan
 
Vera responded:  2017-10-10 14:36
Hi Brendan,

Thanks for your quick reply. I saw default Trypsin (semi) as well, but I was looking for Chymotrypsin Semi and I can't edit it. Thanks.

Vera
 
Brendan MacLean responded:  2017-10-10 14:47
This appears to be only that I missed connecting the checkbox to the internal data structure. So, if you really want something other than Trypsin (semi), then you would need to get it into Skyline through XML, either by editing a Skyline document by hand or an exported Skyline settings file (.skys).

For instance, if you open a Skyline document and locate the enzyme XML, like this:

      <enzyme name="GluC (semi)" cut="DE" no_cut="P" sense="C" />

Just change that to:

      <enzyme name="GluC (semi)" cut="DE" no_cut="P" sense="C" semi="True" />

Then re-open the file and check the Edit Enzyme form. You will find the checkbox checked, and using this enzyme will give you semi-cleavage.

It is really just that on OK of this form, Skyline never sets the "semi" attribute in memory. So, your only access to a working semi-cleavage enzyme is to use the "Trypsin (semi)" enzyme now supplied by default, or using this XML editing hack to create one.

This will be fixed in the next release of Skyline-daily. I will also make the change in the Skyline 3.7 branch in case we make another patch release of Skyline 3.7, but I can't promise we will.

--Brendan
 
Vera responded:  2017-10-10 15:46
Hi Brendan,

I followed your instructions and now it works. Thanks a lot!

Vera