Until top-down proteomics really reaches its potential most of us are going to be doing shotgun proteomics. And it has this nasty drawback. We can make a peptide-spectral match (PSM) but sometimes that PSM can be linked to multiple proteins. Figuring out which one it came from can be hard, if not impossible.
We've seen some good new tools lately such as FidoCT. PIA is a new one and its open to everybody and a bunch of search engines. You can read about it in this new paper in JPR here.
Some of the highlights are that its got an easy interface and it can take data from just about anything. I'm toying around with the web interface now and its got data from MS-GF+ and X!Tandem (and Mascot? I forget now, but I think I saw it, but I don't want to hit the "back" button on it) and some other programs already up there for me to mess with.
The number of metrics it uses to support its inference is a little overwhelming. This is obviously a powerful piece of software. The web interface seems to be more of a demonstration of the power it has and the true software is downloadable and fully scalable from single PC usage to use on servers and clusters.
You can check out the PIA website here.
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