Saturday, September 2, 2017

Open source (free!) software for top down proteomics!

I haven't got to try this yet (27 crazy sleep deprived days to go!) but two people I trust said it's pretty great!

It's called Informed Proteomics and it's a free software package for top down proteomics.

You can read about it in Nature Methods here.

You can get the software here.

Another piece of software I don't think gets enough attention (that I have used!) is the MashSuite. While not as powerful as commercial software like Prosight, it is really user friendly and has some solid features.  You can get it here.

On the topic -- don't forget that there is a free version of Prosight -- Prosight Lite.

This does a great job of allowing you to instantly test hypotheses about your proteoform against the theoretical data.


  1. What takes the most cpu time on this process? How big of a server do you need?

    1. This depends an awful lot on the software -- the kind of file generated (high-high is easier to work with than high-low; and I've honestly never tried low-high, but I'd suspect it falls somewhere in the middle) -- and the depth you want out of it -- in general, however, the answer tends to be LOADS of CPU power -- far more than you need for shotgun proteomics.

  2. The article has specification on the computers used in the benchmarking. It's a reasonably big desktop. Servers are not necessary but something more than a laptop is necessary if you are doing global top-down proteomics.