Thursday, December 24, 2015

CaspDB - A database of caspase cleavage products!

Another tool to help find identifications for unmatched MS/MS spectra!  Caspases are proteins that hang around just to destroy other proteins. They are a critical component of apoptosis and normal cell maintenance, and if you believe the recent in silico protein cycle predictions -- they are active constantly. If my mix of proteins I just harvested is full of incomplete, complete, modified AND degraded proteins, then all these unmatched spectra start to make sense.

Caspases have specific substrates for degradation and a bunch of them have been worked out. CaspDB is a new online tool to help you work with this this information. It is described in this new Open Access paper from Sonu Kumar et al.,.

While the paper is totally neat and all, you can go directly to check out this online tool here.  You'll quickly find out that this tool requires a good bit of pre-existing information before it is useful. Once you've got some data, you can use it to run through your protein of interest and different caspases to see if you've got stuff that makes sense. The paper goes forward to show how awesome these prediction tools are by going ahead and proving that a ton of their software predictions are totally true.

This is obviously a very powerful and interesting tool and this will generate some great data from the validation end. But first you need to get some observations....

...(how did we ever get anything done before this...????...)

Check out this thing!!!  Its called Pripper and, wait, we'll need this... go WayBack to this paper from Mirva Piippo et al., that describes Pripper. Pripper is a Java tool that will take any FASTA database you give it and will perform in silico caspase cleavages on that database and give you a new FASTA that has all the predicted caspase cleavage products.

If you're thinking "How can I trust a tool that is 5 whole years old?" Never fear, it has been updated multiple times (the version I just unzipped is time stamped from 2013). Oh. If you download Pripper here you might want to right click on the zip file, go to properties, click "unblock" then "apply" and THEN unzip it. Windows Defender on my PC blocked it as a threat.

Now you have a tool that will make you a predicted caspase cleavage FASTA that you can run against your samples. If it comes up with something really cool then you can go to the CaspDB and search those observations against their more advanced prediction models (and validated data!)

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