enzyme specificity

[Chia-wei Lin]

Dear all, 

Thanks for creating this cool tools for DSB and XL analysis. 

I wonder if SIM will open to semi-specific search for enzyme in the future. 

In addition, for homodimer, if the protein is not labeled with C13, could we still use SIM to find the DSB by SIM? 

Thanks. 

Best,

Chia-Wei

[Diogo Borges]

Dear Chia-wei,

Thanks for your email. I will explain in detail each question:

"I wonder if SIM will open to semi-specific search for enzyme in the future."

SIM-XL performs a fully specific search for cross-linking identification, because it has been designed to work on searches with non-cleavable cross-linkers. In this case, it requires small databases.

However, when a large database is used, there is a feature responsible for reducing it where SIM-XL uses a strategy to figure out peptides that contain dead-end modification (hydrolyzed bond peptides) in order to create a new database that contains only the proteins inferred by the identified dead-end modified peptides.

This strategy works for both fully-specific and semi-specific searches. And you can use this feature even if you have a small database (We don't recommend it once you will increase the search space, in consequence, will increase the number of false-positives).

To do so, go to XL Advanced Parameters and Enable the option "Dynamic DB Reduction". You can use the fields XCorr Threshold and Min # Peptides as 2.5 and 2, respectively. Afterwards, go back to the main tab (XL Search) and change the "Enzyme Specificity" field to "Semi-specific".

"In addition, for homodimer, if the protein is not labeled with C13, could we still use SIM to find the DSB by SIM? "

Yes, we could.

In this case, SIM-XL will work as the traditional search, i.e., taking into account the protein without labeling.

If you have any further questions, just email us.

Best,

Diogo

_____________________________________

Diogo Borges Lima

About me: @diogobor | diogobor

URL: diogobor

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[Chia-wei Lin]

Dear Diogo,

Thanks for your reply. I was so blind and did not see your reply for months...

For homodimer one, thanks for the information. Does it means that I don't have to activate "homodimer", SIM-XL will anyway consider homodimer?

In addition, I try to install the latest version of SIM-XL but get the error message as other people. Could you have a look? Thanks

Best,

Chia-Wei

[Diogo Borges]

Dear Chia-wei,

You should enable homodimer analysis if a protein is labeled with C13 or N15. If not, you don’t need to enable this option and SIM-XL will still identify homodimers. 

At this moment I’m on vacation and I’ll return next week. 

The current version of SIM-XL contains a corrupted file in our server. That’s the reason you are not able to download it. As soon as I come back , I’ll fix the problem. 

Best,

Diogo

To view this discussion on the web visit https://groups.google.com/d/msgid/simxl/23d0d6e4-5add-44be-b27c-27631cf63e73n%40googlegroups.com.

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[Chia-wei Lin]

Dear Diogo,

Thanks for your prompt reply. Wish you have a nice holiday.

Best,

Chia-Wei

[Paulo C Carvalho]

Where you able to install the software? 

To view this discussion on the web visit https://groups.google.com/d/msgid/simxl/63cacbfd-a233-4df9-8161-38926373ccc0n%40googlegroups.com.

[Diogo Borges]

Dear Chia-Wei,

We have fixed the issue about the download and now you are able to update your version.

Let me know if you have any questions.

Best,

Diogo

_____________________________________

Diogo Borges Lima

About me: @diogobor | diogobor

URL: diogobor

To view this discussion on the web visit https://groups.google.com/d/msgid/simxl/63cacbfd-a233-4df9-8161-38926373ccc0n%40googlegroups.com.