In higher organisms proteins commonly have a ton of different forms. Splicing events are very happy to take a protein that has multiple functions and cleave out one of them to make a more specific protein. Of course...these cleavages occur at the genetic level and don't follow the same rules as trypsin. To detect these events with proteomics you have two choices -- the first is Top Down and the second is shotgun proteomics with a database that knows about the alternative sequences.
ProtAnnot is a new tool described in this open access paper by Tarun Mall et al., that is an add-in for the Integrated Genome Browser (IGB). It highlights your alternative proteoforms within a sequence. I especially like the trick it does with data processing. So your normal session of IGB isn't interrupted in any way, if you choose to use ProtAnnot it fires up an extra thread on your server automatically to do its computations.
If you just can't get the masses of your protein to line up or get that last bit of sequence coverage, this tool might be exactly what you need.
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